Indy is not an IOS reloading game in the way MOHH2 and Mk are. It only reloads the IOS when you play Fate of Atlantis in the extras there is no Alt method for indy only if you wish to play fate of atlantis.
I have Rev13a and just have to turn on 002 fix in GX. You should try NeoGamma if your not on Rev13a, if you are reinstall Rev13a again as I have heard a few ppl having some game issues and reinstalling seemed to correct the problem. If not burn a dvd and run it from a Backup loader or Neogamma and see. If not working then it could be a bad dump