Reporting the same isssue here, and some testing shows that disabling the JIT shader slows the game down too much for it to be playable, although I haven't experienced any glitches or graphical errors. Bleeding Edge 86 remedies the graphical issue, however, it crashes barely a minute into loading the game. BE 42 I'm afraid is simply too slow for my poor GTX 580 to handle
I've also noticed that with the current 'stable' version of Citra (Used in the screenshot), certain particle effects disappear entirely, such as the sparkles over an Event Tile. I hope the good folks working on Citra can fix this soon enough, because they've been doing a fantastic job so far! Despite my so-so graphical power I get a fair 25-30 FPS during combat cutscenes, whilst grid navigation and low-intensity screens are a solid 60 FPS. Cinematic cutscenes even manage an enjoyable 40-45 or so.