This is one of the pitfalls with layering divisions over interactive portions of your site. You've put a barrier between your links and your users which is not good. Without seeing your page, it's impossible to make valid suggestions. My hunch is you'll need to remove the transparent layers, or move your menus to another region on your page.
Thanks for answering!
I'm still thinking that there might be some clever solution for this..
Could it maybe be possible to do this with hotspots/image maps? If I were to create a hotspot on top of everything that would cover the whole button area maybe?
Hot Spots are linked regions on Image Maps. You can't put a hot spot on an empty layer or background image. You need a real image for this to work.
Can you post a URL to your page?