I'd start by verifying that you really are using the same .sts file, book files, and FrameMaker application files. This includes any personal settings in \Users\<username>\AppData\Roaming\Adobe\FrameMaker\<version> .
Ensure all files are on a local hard disc. This will remove any discrepancies caused by the caches that fileservers use.
Wipe any existing output.
Generate new output, and verify the datestamps are for now.
Use something like the Microsoft File Checksum Integrity Verifier tool, or a file comparison tool, to compare all relevant files on the two machines: