I have exactly the same problem as the maker of this thread.
The only difference however, is that my PS2 is modded and I don't have to use swapmagic or bootcd's or whatever. I've been all over the net (and this forum in particular) looking for an answer. tried to rebuild the game, but never got past the part where you use CD/DVD generator (got the stupid "too short location length" error, which noone seemed to have the answer to). I have absolutely no idea what the modchip is called, but I do know that so far, I have never experience with either PAL or NTSC games, whatsoever. I only hope someone can give me an answer to my problem. Help is very much appreciated!
If you mean Star Ocean:Till the End of Time, then I don't think the problem is size. From how you've described it, you're trying to burn the whole game on one disc, when the game itself is two discs, If I remember correctly. If you have one ISO containing data for both discs, it WILL present a problem. Sort of like trying to rebuild God of War 2 from it's original size, despite the fact that it's meant for a dual-layered disc.
Thanks for such a fast respond! I should have mentioned that I do have the two discs seperated, and that I'm only working on the first one right now. So I don't think that's the problem here.