I am glad that you were able to get everything working!
If this does happen again we would like to hear about it. We do recommend creating a new post and post it on the main page here: http://forums.ni.com/t5/LabVIEW/bd-p/170 so that it can receive more views.
OK, I did some deep digging and worked out my issue.
I had a VIP installation that was placing a library into vi.lib with bad links to missing dependencies. When that library was being loaded as part of a bigger project, LabVIEW was baulking at the missing deps and, instead of showing me the usual conflicts resolution window, I was getting this odd notification. One for each bad link.
I resolved the issues in the VIP distribution and now my problem is solved.
If anybody wants further details I can post here.
I've just run into the same issue, but fortunately, I've managed to fix the problem. In my case, there were some files in a library that Labview was unable to locate because I moved those files on the disk. I deleted them from the library, then re-added those files, and the message
didn't show up afterward. Please look into your libraries which you are using in your project if there are some unlocatable files.