Trouble saving in PPRE 0.14 beta

I've finally begun working on a rehack of T-Dub's Pokémon Sol Platinum game. Unfortunately. I've found only one beginner-friendly tool that supports re-hacks of Gen IV games; and that one (PPRE) is still in beta. I have no problem editing and saving Pokédex data in PPRE; but I'm unable to save the other changes I'd planned (renaming some items and reclassifying some moves). Has anybody else had similar problems using PPRE? I'm willing to hear tips and explanations from more experienced ROM hackers.

I've never hacked a rom, but modifying something thats already been modified would seem like asking for trouble to me.

I've tried making the same edits with PPRE and an unhacked Platinum ROM. Same results: the Pokédex changes were saveable, but not the other types. Either the editor is missing some "save" buttons, or I'm overlooking something crucial.