My '98 5spd did that for over 80k miles before I finally pulled the master cylinder out to look at it. The rod was bent. I coughed up $267 green stamps for a new straight one that included the master cylinder, slave cylinder, hose and fluid. After I installed it I was happy that it was all one piece already charged and ready to go. It sure was nice and smooth operating. Quiet too!
It was probably a warrantable item but I waited a bit too long.