Without any detailed knowledge about your program, it's hard to say where the problem might be. If it really is hanging up somewhere, then it would be very important to find out where this hang-up is occurring in your code. You can find this out by either running the VI in highlight execution mode or by using execution stepping. Once you've found out where the hang-up is, troubleshooting should be much, much easier.
Regards,
E. Sulzer
Applications Engineer
National Instruments