wouldn't have thought engine running would make any difference tbh.
could the seals have flipped though if you bled using the vacuum pump???
i wish i could help further but cant i'm afraid i just remember it from changing my brothers master cylinder on his 02 megane coupe which brought some braking efficiency back (as in it now stops) but the pedal still feels crap. could be the fact its french though, i did tell him not to buy it

or the pattern part is the wrong size. he hasn't had any problems though and doesn't hang about in it either but plan is to rebleed it using our new gunsen eezybleeder. never used one before and hoping the pressure might be enough to release any air locks.
incidentally does anyone know how the gunsen doesn't over fill the reserviour? or does it?
sory to thread hyjack fudge but it is sort of on topic