Well, first, just because the tables are always stacked doens't necessarily mean anything is wrong. That could be your desired result.
It all depends on what you want to happen.
The usual way to test if things are working correctly is with the setup in the homepage video. You would use 'Move To Grid' setting = 'Action Required'. Then, Start up SaT and put a table in the Stack slot. When it is your turn to act, the table should move from the stack to the first available grid slot.
If the table stays in the stack and never moves, even when its your turn, then you can be sure that there is a problem.
Whether it is your custom layout and custom deck that are causing the problem, I cannot be sure without seeing a screenshot. Usually, as long as the fold/call/bet buttons are in the same place, then it should be ok.
One thing you could try is to go back to the default FTP graphics, and then remove and re-Include FTP within SaT. Then run the test again. If it works, then we have successfully narrowed the problem and can investigate your custom layout further