I have kind of a same problem, I played my FFIX to the end of the 2nd cd, but when i save it on the disc change screen and reboot my ePSXe (1.5.2) the savefile has disappeared and there is only a file from my previous save (which was at lifa tree just before the ending FMV:s). What to do anyone?
I have a BIG problem !!!
When The Change Disc Screen appears (FF9) I change the disc and it loads but it doesnt finish ! It just makes a sound like *tack tack* *tack tack* each 10 seconds. I tried to start the game directly from CD 2 but theres the same problem ! It doesn´t start at all ! Can anybody help me ? (I have the German PAL version of the game)