Gigabyte boards and serial port problems

I have started to notice a problem with the gigabyte boards I have here and their serial ports. The first time was when I was trying to fit a UPS to a new server based on a gigabyte server board and no matter what I did I couldnt get it to communicate with the serial port! I even tried to on my own workstation (also Gigabyte based) and it still didnt work so I blamed the UPS.
Now I have just received a switch back from 3 Com so I want to program it so after the hassle of getting a null modem cable because there wasnt any in sight I sit down and plug it in and guess what, cannot open com port again! I took the switch and cable home and connected them to my home PC, opened up hyperterminal and guess what connected first time no problem .
So anyone have any experience with these kind of issues?
I have:
Checked the ports are enabled in BIOS and tried all the different options in BIOS.
Checked device manager for any faults.
I ahve upgraded the BIOS.

Any input greatly appreciated