Quicken loses transactions from .QIF. Unsupported? Workarounds?

I use Quicken 2003 Basic (Win XP) for my checkbook and pay bills through my bank’s web site. The web site exports .QIF files which Quicken imports, to record the transactions.
Three times, now, one of the transactions has not made it into my register, making my balance look higher than it is. The transactions get processed - somebody gets paid and it appears on my statement. And the transaction appears in the .QIF file (I can see it if I open the file with a text editor). Each time this has happened with a different payee and the entry appears at a different location in the .QIF file.

So I called Tech Support, and they say they don’t provide any tech support for this product feature. WTF? With more and more people doing online banking, and considering the seriousness of this apparent bug (how many other software bugs can make you bounce a check?), how can they just not offer tech support?

Anyway, does anybody know of a patch or a workaround to fix this bug? Or does anybody know otherwise: that this is not a bug and there is something I am doing that causes the trouble?

Is there anything more reliable and easier than printing out the web site and typing each entry in by hand?