I had my clutch and throwout bearing done about two weeks ago and since then when I press in the clutch, for the first 2-3 inches, the pedal feels "bumpy". (Almost like if you were turning a bearing that has flatspots on the balls.) It also happens when I release the clutch, also for the last 2-3 inches of the motion. (I can slightly feel it throughout the entire motion of releasing the pedal if I release the pedal very slowly.) Finally, this only happens when the jeep is running. Perfectly smooth when the jeep is off.

Thoughts/ideas?

Sry, it's a '98 TJ w/ 4.0L and 5spd.

Sounds like you need to rebleed the system. Should be a bleeder valve on the slave cylinder. It doesn't make any wierd noises does it?