Simply download all of the cores with the most recent nightly, that should update them all.I downloaded all the cores off RetroArch, then updated them. I've done everything that I can do. Must all be sided with the Album then I guess. Screw it, if installing the NSP fixes all these dumb menu and core issues, I will just risk it and do it anyway.
Go fresh with the settings, and try Atmosphere as m4xw said for N64, that should alleviate almost all of your issues.