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Adding this for posterity. After reviewing the project in question, there were 2 problems:

  1. The project was being run from a network drive (where it was saved). Depending on your network security settings, PAT 2.1 may or may not run projects correctly from a network drive. Because network security varies between companies, the easiest way to rule this out is to save the project to your local hard drive and run from there.

  2. There was a measure test whose path length exceeded 256 characters, which is the limit on Windows. This appears in a message in PAT which should include the measure name. If you encounter this issue, you can try shortening the measure's files, updating the measure, and re-running.