PopStation isn't 100% compatible with every game... check out the POPS Compatibility List to find some that definitely do and don't work.
To make matters more complex it's been discovered that Sony built game-specific patches into PopS so using a different Game ID when you turn your PSone game into an EBOOT can sometimes fix glitches... see the thread Resident Evil 2 now WORKING on 3.40 OE for more information.
Specifically the code for the Japanese Resident Evil 2 ( SLPS01222 ) has fixed many of the glitches when playing Brave Fencer Musashi but you may run into other problems further into the game...
By using popsloader you can load versions of pops all the way down to 3.00 on 3.71 M33. There's a good thread on getting it setup here:Is there a way to use a prior version of POPs to play Musashi without downgrading from 3.71 M33-3?