[jgannon]

That's a lot of clicks. I can't promise you that your problem is oversaturating the interrupts, but it's the first thing I would investigate. Plug in your divider board, and use the highest divider you can. If that eliminates the problem, you can go to finer resolution as long as it's still working. I'm sure there are other possible causes for this problem, but they would be impossible to find without seeing your code, and maybe still impossible then. In any case, try that first.

EDIT: Now that I see your latest post, you definitely shouldn't be doing anything in your interrupt handler other than incrementing a variable or something. That would be the first thing I would fix, if you are indeed doing a puts or something in there.