We have two microwaves in one of our breakrooms (the one that I use most often.) I find it mildly irritating when someone is using a microwave for heating one of those meals that takes seven minutes, stir, heat for another five minutes.
My meals usually take about 1-2 minutes. I’ll pop it in and take my bathroom break. If there are other people waiting for the microwave, I’ll let them know they can pull mine out when it’s done (mainly, because I can’t pee in a minute fifteen seconds.)
I’d go with B, as a little bit annoying, but hardly the end of the world.
I was annoyed at work one day in our 2 microwave kitchen when someone had put something clearly frozen in the microwave for 20 minutes and then disappeared. This effectively left 1 microwave for everyone else to use at lunch time.
It’s called small talk. It warps the time / space continuum.
A. Nobody’s using either when you arrive, so using both can’t be rude. Given that you’re not monopolizing both for more than 1 minute, I wouldn’t give it another thought.
I’d go with B. But I wouldn’t really care if I came in there and saw this happening (especially if it was a 1 min wait). I would be bemused though, and wonder why you didn’t just cook BOTH in one microwave. “Who listens to the microwave directions THAT much?” I’d be thinking to myself, probably while watching you cook your food, and I’d take the min. just to observe you*.
*Which I suppose could be mildly rude in itself. 
I interpreted the ‘two minutes’ thing as* ‘food that needs two minutes’ heating, which I break up into two individual one-minute tasks thusly:’*, but on re-reading, it does look like the overlap is 60 seconds.
To me it’s somewhere in between B and C. If I had to wait (a whole minute!) while someone hogged both the microwaves I’d be kind of irritated, but it’s not worth gettting all bent out of shape about.
I can’t believe you would be so rude as to use both microwaves at the same time…no…wait…sounds perfectly resonable to me.
I’m gonna go A, though I think it’s actually better than that since you actually stagger the times to allow someone coming in less time to wait on a microwave. I have actually waited to heat my lunch up and told someone to use both our microwaves at the same time since they had multiple things to heat up. If they get them done at the same time, they can just sit down and start eating without having to wait on everything getting done in one microwave.
So yeah, I think you’re a helluva guy for thinking about other people at all while at the office.
SN1P3