I don't have this issue with 1964mod.
tested with SM64 and working fine switching between fullscreen and windowed mode.
Color is fine too.
window - 1400x1050
fullscreen - 1920x1200 32bit
The only issue I have is that switching back to window mode still retain max window size although it doesn't matter as I get 1920x1200 in window mode instead of 1400x1050 - weird!
Maybe this part is an emu issue or video plugin did not request for resize request when switching back to window mode from fullscreen mode.