I think the best thing to do to try to solve the quake problem, is to build a core version prior to Dec. 20th, and link it to the new Retroarch version, and see if the problem persists or not. I have no way to test these builds though at the moment. I guess I could locate everything needed to use it and test, unless someone else can compile all of this and test it out, before I can. If we can prove the problem is not in the core, then they can fix the issue in the main repo. If the problem is in the core, then we can post the issue there.
BTW, to all people that compile Retroarch, you now need DevKitPPC r29 in order to compile the newest build. DevKitPPC r29 will however break some other things you may already have. Just a warning to you.