I could not duplicate your issue on my computer. Whenever I applied a theme, the button styles changed along with the background.
Have you tried just manually changing the button styles? You can change an entire page at once just by Ctrl+a to select the entire menu page and then double-clicking on the style on the Button menu? It might be easier than trying to find a solution.
Meantime, if you start a new project and change theme, do you have the same issue?