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 Jul 24 2015
J-1.8.0_45. 64-bit
This is a known Java issue. Unfortunately, the only "fix" at the moment is quickly switching to another application then back to TheBrain as you mentioned.

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