Thanks Randall, the problem was related to file I/O. I found a subVI that was using converted LabVIEW 5.1 versions of the configuration file VIs with references opened with the LabVIEW 6 Open.vi. The reference was passed back out and closed with with the LabVIEW 6 close, but apparently there is some incompatibility here that only shows up when the application is compiled.
Matt
