I had a lot of issues with my PC (with Windows ME at the time) - I could synch and install upgrade files, but logo uploading worked 1 time out of 10 and MLord's patches never worked. After checking everything on my PC many times, I used a version of download.c for COM2 (which was identically set up to COM1) and now everything works. I could find no sensible reason for it - no resource clashes, the ports all work fine for other apps etc.
So I would recommend trying another port just to see if it works:)
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Rory
MkIIa, blue lit buttons, memory upgrade, 1Tb in Subaru Forester STi
MkII, 240Gb in Mark Lord dock
MkII, 80Gb SSD in dock