Thanks for your reply Xaq. Sorry it's taken me so long to reply, but this issue sort of got pushed to the bottom of the pile. I finally found the solution to the problem and though I would post it in case anybody else runs into a similar issue. I implemented your idea and extended it so far as to look inside of arrays and clusters as well. Unfortunately, this did not reveal the root of the problem.
It turns out that the problem was not with the application at all, but rather an OS issue. I was updating XControls in a VI running continuously in a subpanel. Because the variables in the XControls could be changed by the user I was constantly updating its properties, one of which was the tip strip text. Once I removed this property update the program worked just fine. I'm guessing that the OS generates some sort of interrupt that causes the program to briefly lose focus.
Moral of the story: Updating the Tip Strip property of a control will cause the key focus to be lost. I have only tested this for XControls, but I'm assuming it is the same for regular controls as well.
Hopefully this will provide some help to others later. Believe me it was no fun to troubleshoot.
Thanks again Xaq.