Have you installed the latest LVUpdate and reimaged both the cRIO and DS?
http://joule.ni.com/nidu/cds/view/p/lang/en/id/1180
If you have done the installation recently, my understanding is that you'll need to open a new FRC project and "import" your custom VIs. Without going through the "new project" process, you may have some bad links to sub-VIs.
Another option is to press the broken run arrow and let LabVIEW point out where the problem is. It shouldn't be too hard to track down the issue.
Russ