Are you storing templates as files? I've read recently that they had issues with these updating. If so, try turning that off (to get it to come from the database) and then turn it back on. Or flush your cache.
I'm working on this too but it seems that if I don't set a background color, xenforo applies a different color if I pass the mouse over the buttons.
However, if I add a background color as yolulz, the hover color disappears the same as the blue background on "post reply". All buttons use the same background and I can't differentiate the primary one