Are you using the VI Path property, using a reference to the current VI?
I could be wrong, but if you're attempting to use a path relative to the current VI, I think that does indeed change in a built application. If your VI used to be C:\somewhere\foo.VI, then after building its path would actually be C:\somewhere\foo.EXE\foo.vi . Thus, if foo.VI used to try to make a folder like C:\somewhere\datafolder, the built application would be trying to make C:\somewhere\foo.EXE\datafolder , which wouldn't work.
This is sort of a shot in the dark, but does this sound like it might be the case?
EDIT: Dennis beat me to it.
Message Edited by kehander on 10-16-2006 03:26 PM