A few people - myself included - have had issues switching from Disc 1 to Disc 2 after the Plane Tyrant fight.

Apparently this is a known issue, particularly when using a ROM of this game.

The solution is to make the save when prompted directly after the Tyrant fight (this does not count as an actual save - you will see it registers as save 00), restart with Disc 2, and load that save.

Annoying, but no negative effect on IGT so it's a solution.

everyone my 2 jp discs on code veronica fixes the change disc error now so if you guys need any more info on this please speak to mogul thank you

So apparently the fix here is to have each ROM in it's own folder within the games folder - As mentioned above Mega figured this out.