The problem is probably that the Sit&Go tables aren't getting correctly detected by SaT as being poker tables, therefore nothing is working on them (hotkeys, table movement, etc). This would make sense why New Tables aren't going to slot1. They are probably just opening wherever the poker client puts them. What Site are you playing on? Can you post the table titles of both a cash game and a sit&go? Something like this:
Pokerstars - Table Bigfoot - $2/$4 No Limit Holdem
Pokerstars - $100+10 Sit&Go tournament 123456
etc
Pokerstars - Table Bigfoot - $2/$4 No Limit Holdem
Pokerstars - $100+10 Sit&Go tournament 123456
etc