Can't rotate anything

I’ve been pulling my hair out over this for the past few days, and I can’t come up with any good solution. Basically, I’m trying to play Banjo-Tooie. So, I went ahead and downloaded the latest nightly zip (1.3.3 according to the app), installed 1.0.0.1 from Cydia, overwrote RetroArch.app with the one from the zip, and resprung. And then I opened the app and I let it update everything. I already tried the latest stable and had the exact same problem I have now. The app seems to be working fine. However, whenever I load the game, it loads, but it does so with the PSX overlay, and it also loads trapped in landscape mode, with the game itself taking up about 2 square inches at the top of the screen. Just rotating my device won’t rotate the app no matter what I do (no, I’m not on orientation lock) and I can’t for the life of me find any way at all to force it to load using the whole screen. Using the built in “Rotation” option doesn’t do me much good either; it rotates the game, yes, but not the window. I end up with half of a sideways game, still stuck at the top of the screen. To correct this, I tried expanding the resolution under core options, but it just expands the internal resolution the game runs at, not the literal resolution in screen pixels. The custom viewbox X and Y options don’t seem to do anything at all.

I have tried just using 1.0.0.1 out of the box, but that version doesn’t play well with B-T; it gets stuck on the title screen forever saying “No Controller.” This is a known bug that was fixed in 1.0.0.2. I’ve also tried manually replacing the Mupen64 core with the latest one (Mupen64Plus 2.0-rc2) on 1.0.0.1, but doing that just brings even more resolution problems, either making the box short and stretched or putting 80% of it offscreen. Any help here would be VERY greatly appreciated.

iPhone 5s, TaiG Jailbroken 8.4

As an extra note, I am using LittleBrother set to the iPhone 6 resolution, but I don’t see how that would affect this.