I have a link between a baystack switch and a cisco 1841 router, I have the same setup and same configuration at 70 other sites and have not seen this problem before.. when each device is manually set to 100/full the link goes down and I get no lights on either end, when one end is set to auto/auto and the other manually to 100/full the link comes up as100/full for anywhere between 10secs and several hours then drops back to half duplex. when both ends were auto auto they came up 100/half, I set the duplex on the switch only to full then the link was running 100/ full, I tried manually setting the speed/duplex when the link was running correctly but that killed the link again and I couldn't get it running back at 100/full again.
I have tried different switchports and it has the same problem, is it possible for a device to mis-report what duplex its running at? we are going to replace the cabling to ensure its not faulty but because it was able to run at full duplex it rules out a dodgy pair in the cable.
at all the other sites we have 100/full statically set on the interfaces at each end.