technically you can put the throw out bearing on backwards and it would still mount up correctly but you wouldnt be able to shift at all, your prolly right though its most likely a hydraulic issue, so just go and check all the usuals, clutch master cylinder, clutch slave cylinder, all the lines, maybe somehow its not pushing the cylinder shaft into the throwout fork enough at some point and then it gets the full force, it sounds like a weird problem, just investigate i guess.......