In my runs in the past, I've encountered problems with my PS2 failing to load the first FMV of each disc that have forced me to reset the game, costing valuable time. You can see what I mean at the times 2h 56m, 6h 9m, and 11h 8m of my all bosses run. I've done some experimenting and found a fix that seems to resolve the issue, but I want to check first to make sure I would be allowed to do this in a run.
My fix is that, shortly after the game starts playing from a new disc after swapping, I simply open the disc tray and close it again. This seems to make everything run smoothly for some reason. I'm positive this doesn't give me any advantage compared to other runners because nothing else is affected in the game as far as I can tell. Can I go ahead and incorporate this fix into runs that I do?
As long as you arent skipping anything while the disc tray is open (using it to skip the FMV for instance) then technically yes, its fine.
That being said, it sounds like you have either an issue with your discs, or your laser. In either case, I'd suggest looking into it. Both issues can get worse over time, and may cause you even more problems down the line.
FF9 Discs are still pretty cheap if you need to replace them.