EDIT: I ended up solving this problem by trashing my preferences. Now my plugin and vsti gui’s stay on top of the screen, both on the project page and in the mix console, as they should and all is working well. My problem was quite serious as the plugin windows were disappearing even when the system was idle, so I am very happy to have it fixed. 
I have this issue where my plug-in windows, or any other window for that matter, keeps disappearing. This happens when I am in the mixer or on the project page. Plugin Gui’s just vanish behind the main window (project window or mixer). I hope I am not alone in this or maybe there is a possible fix? FYI, I do have them set to always on top.
Any ideas or suggestions would be welcomed.
Don