As odd as it may sound, I once saw a similar problem on a project and it only happened when a specific version of the proramming (pof) file was in use. If you were lucky, you could see a few pixels "blinking" on the screen -- a really cool side-effect!
After recompiling the project in Quartus with all settings targeting "speed" rather than "area", the problem vanished. In this case, it was purely a hardware problem.
Why do you think this is related to FLTK? When you compile a plain nano-X application, don't you have the same problems?
Cheers,
Ricardo.