Without knowing exactly what your hardware is, it's difficult to say exactly what your problem might be. But a place to start might be with the application's overall structure. First of all, a sequence structure isn't required. The 5 steps you mentioned all have a natural data dependency on the step before it. Specifically, did the step work or did it return an error.
So, as a first step in the troubleshooting process, lose the sequence structure and tie the VIs that are implementing each of the steps (you do have those actions encapsulated in subVIs, right?) together using the error IO. Now run the app and see if when it misbehaves there is an error.
Also could you post our code in V6 format? That will help in getting a more detailed answer.
Mike...