Hello, Relisus. I played both 3 times each on epsxe and never saw anything like that. But when played Final Fantasy 9 I had a lot of problems, one of them resembling this, that I solved just using a older version of epsxe. (Yes, older). If I remember well, 1.6 gave problems to me, so I changed to 1.5.2. Same thing with Alundra 1. Try that, at least to pass the Sindar Ruins. Which version are you using? It's Windows?
But... it really looks like a media problem. You made a copy of the disco? Can't you make a iso with the disc and then use the iso? Just another suggestion!
Tell me if it works!