Got to this party late...
jb101 - are you using a dual monitor setup?
Reason being, I have the track view on the left monitor and the console view on the right monitor.
(X2a Producer, 64-bit)
If I open the GUI in an FX bin it sits on top of the console.
But click on the console or track view and the GUI slips behind the console.
(I can shrink the console, or drag the top of the console screen down, and there behind it is the missing GUI...)
If I drag the GUI over to the left monitor, it will remain on top of the track view, even if I click on something in the console or track view.
I end up doing a lot of GUI dragging, but if I need the GUI to stay visible, this is how I have to do it...