It appears that the AlgoWizard removes parenthesis on Signals in order to simplify the logic. While logically the signals will work the same, the parenthesis help make it clear to the observer what's going on, and it would be nice if they were not removed automatically.
The parenthesis aren't missing in the sense that the logic is changed. They are just missing in the sense that when you put them in and if they aren't necessary to maintain the logic, SQX removes upon reload of the strategy. At first it was a little disconcerting as I was using the parenthesis to make obvious which logic is grouped; however, I've learned to just accept the current behavior.