Hydraulic throwout bearings are rarely restrained in movement. If you pump the master cylinder or it is too large, you can force it apart and cause it to leak. In every case I know, they give you stroke distance and the master cylinder incorporates a 'stop' so it can't send more fluid than is required.
If your new master cylinder produces more fluid per stroke, it could have easily exceeded the specs on the bearing. When I added the hydraulic throwout to my car, I also added a stop to the master cylinder. I then adjusted the stop so the bearing moves just the amount required.
Not saying this is your issue but it sure is suspect.