Found it!
It was the Keikyu line Umeyashiki station.
The train is 6 cars long, but the station is only 4 cars long.
Apparently this is called a “Selective door operation” or ドアーカット.
The Densha Otaku have been busy uploading stuff to youtube 
After I posted I immediately thought surely they would have figured that out so the platforms must be the limitation. 2 more cars on sardine-day would make it impossible to get off the train if you were stuck in the cars outside of the platform. People would have to know that ahead of time so only the last-stop folks are up there.
Why can’t they just unload the first four cars, scoot forward by two, and unload the last two?
It might work but you lose some of the time gained by not trying to cram people into the train. If the train has to close it’s doors, move forward and open them again there is a loss of time doing this. A time study would answer the question.
It’s hard to imagine that every combination has not been thought out but who knows.
To most Americans in particular, I think this would be true for their impressions of many non-U.S. places. Even a friend who moved from a big U.S. city to mid-sized U.K. city remarked that the Brits seemed much more prone to (1) eating their meals within a fairly narrow window of time (compared to America where in some cities people will make dinner reservations any time between 6:00 and 10:30) and (2) the holiday thing. Or think Continental Europe, where it’s my impression they’re significantly less likely to schedule the big family holiday in June or July (as opposed to August) than in the U.S.
You’re of course right about the Japanese holiday schedules, likewise. I can’t imagine trying to travel during o-Bon or Golden Week, but they gladly endure that because “it’s when the company shuts down and you take a holiday.”
The flip side to all of this is that if you are not culturally or vocationally stuck on JP time, avoiding these very narrow windows of peak congestion means avoiding the massive crowds; even on the crowded lines, I’ve never experienced the sardine-can deal on Tokyo subways or commuter rails, but I’ve just so happened never needed to be on them at 8:45 a.m. or whenever is right before the consensus work start time (these apparently being taken seriously enough that a colleauge whose start time was 8:30 had to call her boss if she was walking into the lobby for the elevator at 8:29 and worried that it might take two as opposed to one minutes to get to her desk). (N.B. that avoiding massive crowds doesn’t mean having the train to yourself – in the aforementioned Shinjuku Sta., where I got stuck waiting for someone for 45 mins., the flow of people is relentless at any time of the day/weekend, and I’ve rarely gotten a seat on, say, the JR commuter train that passes through there).
(BTW, the flip side to my go-off-peak-to-beat-the-crowds ploy is that as in many countries where there is a “right time” to do something you may deke yourself out by going “off peak” as places may keep seasonal hours to a greater extent than Westerners are used to – by analogy I remember a brilliantly-planned (ahem) trip to rural France and the Cote d’Azur in late November. I had the place to myself. No, really, I was completely unmolested by . . . any open restaurants, lines at the (shuttered) tourist destinations, etc.).
They don’t gladly endure it, it’s just the only way you can get a day off because you literally can’t work when the whole company—and every other major company in the country—is shut down. You don’t really have any choice about it; it’s just the way things are done here. Believe me, they hate it almost as much as I do, but they don’t see any alternative other than unemployment and/or homelessness. Doesn’t matter where you work, the conditions are the same at virtually any other company.
Somewhere around my second or third year here, I remember thinking it was hilarious when someone was comparing vacation time and work hours in various countries. Japan’s average was supposedly 43-hour work weeks (if I remember right), and standard was 10–20 days of paid leave. The US’s numbers were slightly more favorable (41 or 42 hours a week) but usually got less vacation; 5–10 days. I thought it was hilarious because someone actually believed the figures they got from Japan.
Everyone—and I mean EVERYONE—works more hours than their official ones. “Temporary” workers typically have contracts that stipulate they can work up to 39 hours so that they’re not considered full-time workers with all the resulting benefits. They are routinely “asked” to stay until 6:00 p.m. even when their work hours end at 5:00. They get an extra hour of pay (usually, though not always) but that extra hour is culturally considered a requirement even when the law says otherwise.
Salaried employees routinely work 60–80 work weeks. A couple of my foreign friends work as regular employees at Japanese companies. They get dirty looks if they leave before 10:00 p.m. They’ll easily pull 4 hours of overtime every day, all year long. Occasionally, they’ll even get paid for it. Company policies dictate what hoops you have to jump through fro that. One of my friends has to stay until at least 7:00 p.m. for any of the overtime to count. If he only stays an hour or an hour and a half past his official working hours, it doesn’t count. If he doesn’t log weekly reports detailing what he was working on (sometimes nothing because he didn’t have any real work to do, but sure as hell couldn’t leave the office before the boss did) he doesn’t get paid for it.
They may get 10–20 days of paid vacation according to their contract, but no one gets to use all of it. Sometimes, they don’t get to use any of it. Taking time off is very, very strongly discouraged. And it’s not uncommon for there to be no sick leave, so if you’re sick, even if you need to go to the doctor for something like intestinal surgery (true story, though not mine) you’ll have to take it out of your paid leave.
At my job, I supposedly get one Saturday a month off (Saturday is normally a half day) except that there’s usually something extra scheduled for that day that requires us to come in. Sometimes there are things scheduled for Sundays, including mandatory trips and retreats. Usually we get a day off in lieu, but even those days might end up going unused because of the schedule, and because taking any time off—even if it’s owed you—is frowned upon. I’ve had 9 day weeks. Legally, Japanese companies only have to give full-time salaried workers 4 days off a month, and that can include legal holidays. When I left my last job, I was owed over 40 days of paid leave, because I was simply unable to take any of it. I still can’t complain that much because if you look at my daily work hours, my job is Happy-Happy Funland! in that I usually get to go home almost on time; usually 30–60 minutes after my official quitting time, rarely more than 2 hours late.
[American] Light Rail Operator chiming in here:
Track maintenance is extremely important. In our system, if there is an issue (broken rail/switch, something on the right-of-way, damaged overhead wire, etc) it not only takes time to fix, but in the process of fixing it, the schedule really gets fouled up. In our system, if there is maintenance work on one track, they have to divert trains to the other track. But the trains in that direction are also using the track, so they have to ‘alternate’. This is known as Manual Block System. In the BEST of circumstances, trains are going to be late because they have to take turns getting past the obstruction/maintenance, etc. That’s not taking account human error (most of the ‘oops’ stuff that happens in Light Rail happens during these unusual situations where trains are crossing over against the current of traffic).
In our system, there’s only about 90-120 minutes during the day that one train or another isn’t traveling around a given stretch of track. That’s not a lot of time to apply ballast (rocks), inspect the track, inspect the overhead, make sure some drunk isn’t passed out around a blind corner, etc. The more time they have, the less likely something is going to fail during a busy time of day.
Our system is tiny compared to the Japanese coutnerparts. On our busiest day of the year we probably move 100,000 people, with about 40 light rail trains traveling on a mere 42 miles of trackway with 7-15 minute headways.
When I lived in Japan, my normal weekday commute to campus took me through Shinjuku Station, and I usually was going through there on the weekends, too (on my way to Harajuku, often). If you have not spent time in Japan, particularly having experienced the busiest train station in the world, it will be very hard for you to conceive of just how many people go through the system every day, especially during peak hours.
I wasn’t always traveling during rush hour, and I still ended up on some very crowded trains–I’ve commented that I wasn’t every worried about a crash, because we were so packed in, no one would move at all. I once saw two men get into a fight because one of them was reading a manga while standing on a very crowded train, and the other guy thought that was incredibly rude because it was invading the space of everyone else around him. Reader got off at the next stop and Yeller followed him… as the train pulled away, I saw him getting up in Reader’s face, and there may have even been the start of some shoving.
I lived in Tokyo* before I visited New York, with the result that when I was in NYC, it looked pretty deserted to me. Out on the street after midnight, there were some people out, but compared to the swarms that were out all night in Tokyo, it was like a ghost town. Part of that, I’m sure, is also related to the way culture has developed around the train schedules there: because the trains stop running from about midnight to five a.m., most events either (a) finish in time for people to make the last train, or (b) start late and then run all night. There were plenty of times that I would go in to see a show starting around 10 p.m. and not come out of the venue until 6 a.m. the next day.
*Okay, technically I lived in Kawasaki, but my university was in Tokyo and I spent most of my time there.
My commute every day by train was over an hour each way, total, and it was solid development the whole way. Roofs after roofs after roofs, stories tall, mile after mile. I used to stand at the front of the trains just so my eyes could look down the track and focus on something farther than a block away.