If you do a search on this forum you will find this to be a common and vexing problem. I myself had this same exact problem about a year ago, and it took me the better part of a day to track it down. As you will find by reading the various threads on this problem, there seems to be no specific cause for this, and it remains a mystery, and the solutions are no better than chanting voodoo, and probably just as effective.
One thing you can try is to force a recompile of your VI hierarchy. Open you top-level VI. If it's set up to run when opened, stop it. Hold down the Control key and click the run button. This will force a recompile of the application. Sometimes this works, sometimes it doesn't. Like I said, voodoo.
Another thing to look for is to check if you are using any diagram disable structures or case structures with a constant wired, as in trying to use the case structure to comment out code.
Are you using classes and passing by reference? There was a mention of this
here.