This is something I experienced some time ago on a project that really put me through the ringer. We worked with NI R&D for 6 weeks at an elevated support level to finally get to the bottom of the issue. The symptoms were my front panels (both in code and exe) would become 'detached' from the block diagram. In other words, the GUI would appear locked while the code behind was actually executing just fine. CPU was very low (3-5%) on all cores. For a long-time monitoring application it was especially problematic as the user wouldn't interact with the GUI for long periods of time; the information on the display would simply quit updating and it would be difficult to detect the condition.
The solution ended up being something out of left field - the Windows Aero theme, which is default for Win 7. R&D finally stumbled across this and was able to turn the issue on off by changing the theme away from Aero. I gave a presentation at NIWEEK just recently and it seems I had 3 people in the audience that were experiencing this same/similar issue. Therefore, I thought I would post this and maybe I could help some others.
All LabVIEW versions including 2012 are affected it seems. I was developing in 2010 at the time, but R&D tried many versions to see if it was version-specific.