I've used checkboxes for a lot of the options instead of buttons (seemed more natural to me) with my app auto-sending the options when it first detects Audiosurf.
Have you had any issues with fullscreening/minimising at all?
This is the biggest thing delaying mine, whenever I drop it out of fullscreen things tend to go hideously wrong.
If my app does it, the wrong screen-mode is selected on the desktop until you click in a window (it actually goes from Audiosurf -> Desktop resolution -> Audiosurf resolution -> Desktop resolution -> Audiosurf resolution, waits for click -> Desktop resolution, which is pretty weird and more than a little annoying).
If I do it manually it drops back to the desktop then instantly back to audiosurf and loses the mouse cursor (so can't click on anything) and alt-F4 is needed to kill Audiosurf.
Following a quit like that, very often the next instance of Audiosurf I run refuses to return messages. It still accepts them but won't return any data. Very odd. Clears itself after about 10 minutes which is even stranger.
Anyway, will have a play with your app, see if I can reproduce the problems or whether it's something I've done.
Might just be this install of Windows, needs re-installing.