You need to use the Mednafen debugger:
- Press ALT+D to bring up the debugger.
- Press the S key to go into step mode.
- Press S to step through the assembly instructions until you are on the instruction right before the tst instruction.
- Use the Arrow key to navigate over to the register R2 and press enter to enter a new value.
- Change the value from 00000000 to 00000002 and press enter.
- Press R to resume the game and that should get you past that issue.
- Press Alt + D to close the debugger.
Also, keep in mind that Mednafen makes a checksum for your disc image and puts that into the save file names. So it wont realize that Disc 2 is Disc 2 and will instead think it's a new game and make a new set of save files for it. If it does this just go into the sav directory in mednafen and rename the Disc 1 files to be the same name as the Disc 2 files, and delete the Disc 2 files.