James,
I have seen a similar issue with regards to running in a runtime environment. Perhaps my experience can be of value.
Try doing a save all on the top level VI. Be sure that none of them are read only or archive, which often happens in distribution, especially to a CD. Try writing a batch file that sets the attributes (attrib *.* -r -a /s).
This may help. Please let us know how you do.
Good luck
Almost forgot, check your hierarchy and check the option to view the full VI path. Go over each element and be sure it is in your library or directory structure. It is quite possible that you are calling something from within the labVIEW directory unwittingly and this can be very problematic.