Hi Conrad,
We faced similar issues and I raised the same on this forum but so far not heard an answer to this query.
We are currently NOT using the sync tool and updating TUBs using the old way (applying in BSI and SAP 000). But I do understand that can be done only up to April 2015 when SAP stops releasing OSS notes for TUBs.
Hope we have the issues sorted out with sync tax tool at the earliest.
Regards
Ruhail