If I go to the preferences menu, make a change to a setting a then OK it takes 10-15 seconds for the preferences window to close and then all the menus on the main menu bar (File, Edit, etc) are greyed out.
If I do something that opens another menu window (e.g. Open Notes Window) or I flip to another App and then back to TheBrain then the menus are visible again. It looks like it is a screen refresh problem.
I am using a MacBook Pro with:
Free Edition Pro Edition trial
126.96.36.199 Jul 24 2015