If you use “Close application to Tray” when restoring it, the Windows Task Bar becomes hidden, if you use “Minimise application to Tray” and restore it, the Windows Task Bar is shown correctly, is this intentional? It’s just kind of annoying, that is all when you are trying to switch to other applications using a mouse.
I’m having this exact same problem, if anyone has a fix, please let me know. This is really annoying and is the one reason why I have not switched over completely to this application. It even hides the taskbar when you click on the icon on the taskbar to minimize & restore from tray.