Thank you for the report, and apologies for not having had a chance to look into this hitherto.
I will need some more detail before I am able to look into this, especially as loss of synchronisation issues are usually very hard to track down. Do you have a version of Pak.256 that you can download in which these multi-tile buildings are present? If so, are you able to describe the circumstances in which the server and client will lose synchronisation in this case? It would also be extremely helpful to know the answer to Dr. Supergood's question, as this will help to narrow down where the problem is occurring.