Figured it out. Thanks to the guys in #macdev on freenode, they noted that a line of code I was using wasn't needed:
[self.window.contentView setWantsLayer:YES];
I wasn't really using the layers so that doesn't need to be set.
Once I removed this, the button colors worked fine in that window. Note: they also said if I did need to use layers, I'd have to set the button's layer's background color to get it to work.