Strange problem. Did you guys try the standard fix of reimporting the mapping twice with the big import button? Maybe try importing layout settings with the tsi (one of the tick box options with the big import button).
Using the TP1 VCI-100 mapping with TP2 changed my layouts when I did something, I can't for the life of me remember what it was though! It turned out to be an easy fix with a couple of command changes in the mapping. Have a look through and see if there are layout commands in there.
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