Depends what you need to burn it on. How big is the ISO? What method of modification are you using to play it? Swap Magic, a mod-chip, ulaunchELF or what? And no, I never backed up RPG Maker 3. If you're using Swap Magic, make sure you use each disc appropriately. Swap Magic CD for PS2 CD-based games with a blue-colored back and Swap Magic DVD for PS2 DVD games with a silver back. You mind listing the contents of what's in the ISO? You can easily get a TOC listing using Expert's tool LBA extractor. Also, what DVD media are you using? Sony, Memorex or so forth.
Try using Sony and see how that goes since you can get it at a nearby store. Unless the media ID on those Memorex DVD-R you are using turn out not to be CMC MAGs, which you could check here, then I don't recommend using those Memorex DVD-R for burning your games onto if they are indeed CMC MAGs. If you can't order DVDs online like at supermediastore.com for Verbatim or Taiyo Yuden, which I would suggest getting either one instead of using Memorex, then go for Sony unless you can get Verbatim instead. Also, is there a possibility that there might be a dummy file you haven't shrunk? How many copies so far have you burnt so far? What PS2 are you using? a fat or slim?
My ps2 is slim, but indeed it must be the media dvds I am using since I also noticed some other problems in other backups, for instance my .Hack//infection and mutation backups start to skip and had long load times after some hours of gameplay never happened to me with the old media was using(TDK)
Usually the problem is using bad quality media, but it could also be something else, however, using top-tier quality DVDs can eliminate one questionable element of the game not working properly.
