Orright, are you sure your UPS is on COM2, and not on 1 for some reason?

No, on second thought - you seem to have OS problems with 1 anyway: since you reckon COM2 is OK, why not knock off the UPS s/w for a short while and then try to use the 2 port for an upgrade? This would let you upgrade (quick fix), verify COM2 (which you think is OK) and means there is some other issue to look at.

Can you say anything about MB/BIOS of your system? Have you got the port settings on Auto in the BIOS? Any other info you can give regarding the physical and low-level setup?