Hi, I'm speculating here but I just recently fixed a similar sounding problem I had with the mouse and keyboard. they would work fine at first but then start exhibiting terrible lag times.. I eventually found out that the mouse and keyboard (both USB) were using the same IRQ as my Wireless network card (which is not working yet). I found this out by typing this:
# cat /proc/interrupts
I think you have to be root to do this. When you give the command it will list all of your IRQ's (16 of them plus NMI and ERR) and devices are using them.
If it looks like a device might be sharing an interrupt with your mouse/keyboard, try moving the offending device to a different PCI slot. It didn't fix my wireless problem, but it sure solved the kbd/mouse problem!