I had this same situation pop up a few days back. I went to log on a character in Felwithe and had the "zone files may be corrupt, try a fresh install" etc. text box pop up. Freaked me out.
I restarted the computer and had no problems. However, I logged out of the game and ran a Registry cleaner and had something like 14 registry link errors that were repaired. In fact, every time I play the game and clean the computer later I come up with a few registry errors. Simply from playing the client w/ launcher, nothing else being run.
I'm uncertain what the interaction of the client and launcher may have but I suspect that something is up. Short answer is - clean / repair the comp every week or so and see if the error keeps showing.
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