Tim,
This is an all too common problem when building an application to load, and then run non-built VIs - the only real solution to the shortcomings of the app builder.
However, the solution is very simple.
The VIs MUST be in a directory structure that is identical to the target structure. This is because VIs are saved with a location. That is, callers look for their subs in specific locations. When you move these files, you loose 'contact' with it, and the caller becomes unexecutable.
Try rebuilding your development directory structure to match the target, opening all files, and reclosing them to save their paths, and then rebuild your install shield. You should have no problems.