I believe I have exactly the same problem since last night, when a Windows update installed that took quite a long time (think it's the "anniversary update") to complete.
Windows 10 Home (14393.rs1_release.161220-1747)
WindowBlinds 10.5 (029 - Windows 10 Edition) - 64 bit OS
It doesn't affect all windows though - mostly message boxes are affected, along with the "Run" dialog box, and various non-maximized windows. I use TightVNC frequently and the connection box and main window suffer the problem, as does PuTTY and even the WindowBlinds configuration window. My guess is that it affects pure Win32 API applications as things like Paint and Explorer windows seem OK. That said, Skype has a thin white bar that covers up the menu.
I checked for WindowBlinds updates but there don't seem to be any.