save the game using what, save states or memory card saves? are you using the disc to play or are you using an image of it and have you attempted to use other emulators like psx to test if this is a reoccuring issue?
I am playing from an image, as I do not want to risk scratching up my discs. It does the same thing when I do use my discs.
Saving by the game's built-in mechanic is what freezes the game. Save states are fine. However, when it brings up the save screen (at a telephone), the game freezes. So, as it stands, I cannot play through the game with traditional saves and I cannot pick up items from chests and lockers.
The game does work properly in pcsx, as I recently found out.
is it the game that freezes or does the emulator itself become unresponsive? for example, can you return to the GUI with the escape key after it freezes or do you have to do a manual shutdown via task manager and restart epsxe in order to get things working again?
if you can still control epsxe when the freeze occurs, return to the GUI and try taking a screen shot of the logger window because it might say something about where the problem is coming from.