When I set the visibility to 'Never', it still pops up when I enter an instance. I can double click 'Let SexyMap control button visibility' to get it to hide, but I have to do this on each log in. I've reinstalled SexyMap a few times, but the issue is always present.

You probably have another addon interfering, try with only SexyMap enabled.

I disabled all other addons and the issue still exists

this is probably a standardized answer, it is always another addon: D

Should be fixed by 403b5b9