Try replacing and properly bleeding the clutch fluid... I replaced the clutch master cylinder and the problem didn't go away, but I don't remember having a problem once I eventually bled it *properly*. I think having a short shifter at the time amplified the problem, but wasn't the cause of it.
It still does it now, but *only* if I'm lazy on the clutch (ie don't press it far enough or fast enough; totally my fault).