I've been having this bizarre issue in FPse64, where if I go into the menu to enable/disable the on-screen buttons, a lot of the times, some random buttons will enable themselves, even when they weren't before, and will often randomly disable others that were previously enabled.
This doesn't happen unless I go into that specific menu at least, but it's very strange. Don't have this issue in the original FPse.
Also, a bit off-topic but I don't think it warrants its own thread, but Legend of Legaia seems to have some issues on FPse64 that aren't present in the original FPse. Namely, the audio seems weirdly sped up at the start of random battles, and happens again at certain points during the battle music loop (have tried using both normal and fast audio plugin, no difference). Also, sometimes the battlefield will briefly flicker black when selecting your moves. I have had some issues with some games' save states imported from the original, but even when I just boot the game normally and load from a memory card save, the issues persist. Have not had these issues in the original emulator, and I'm using the same settings in 64.