one possibly cause of this i've encountered is the polling rate of either the USB port you're using or your mouse could have dropped to 125hz, hence a choppy feeling with normal FPS
try looking for a program called "usb mouse rate", it should tell you what your polling rate is. you basically dont want to have below 500hz (although i've heard of some people liking 250hz)
edit: you could also try capping your fps at a lower, more stable rate to see if its fps fluctuations causing it and launching a map on a local server rather than joining an internet server could rule out internet problems (map cp_badlands in console)