Currently, when I click the LiberKey Tools button, the pop-up menu appears behind the main program. Also, the drop-down menu from any of the 3 tabs also appears behind the main program window. Any ideas?
Update: I have discovered that rebooting does fix the problem, I will continue to monitor to see what does cause the problem when it occurs. Note: I am running WinXP-SP3 on a Dell 8400 w/ 3GB memory.
Update 2: I am now running Ver 5.0 build 0901 and the problem still exists. The problem occurs when I launch ATI Catalyst Control Center, my video card manager. I use this to control primary and secondary monitors. Problem clears when I reboot.

Recently I had the same problem - in my case, before it occurred I had installed the game "Machinarium". After uninstalling the game and rebooting the computer the menus went back to normal. As you can see, I cannot really provide a (proper) solution, but maybe you can narrow down the cause more easily?