Recently I encountered a problem with a WS-x5239 card, this is a Catalyst 5000 with SW ver 6.3(3) it has 2-5012A cards and one 5239 card in slot 5. I moved 3 lines from the 5012A card to the 10/100 5239 card, the systems were working ok on the 5012A cards at half duplex at 10.
I switched them over to the 5239 card and hard coded the port to 100 Full. The NIC cards are on Linux O/S with the latest NIC Drivers both Intel and 3Com cards which can do both 10/100 and Half/Full Duplex. At first we hard coded the NIC to do 100 and Full.
According to our equipment the card on the system would switch to Half Duplex with the port staying at Full.
To trouble shoot further I moved the port to half Duplex and the card would stay at Full, one instance changing the NIC solved the problem the other instance when switching the card did not work I set the port to Auto and it started to work.