See: http://fold.it/portal/files/chatimg/irc_308854_1382569638.png
Black outline around the cookbook and behavior boxes. Not part of it you cant use the outline to drag it.
And a strange text in the competition box: default showing over it.
The Text default was from the track box. The weird outlines appeared after changing puzzle.
It looks like the remembering of the placement of the boxes is fraud if you run in a different window size as the standard that is used when you start up foldit. Then it does not use my whole screen, first thing I do is set it to use the full screen (and then the position of the boxes dont make sense anymore).
I had the same but with the default track box on the puzzle (I was not able to click on the puzzle because of this). Solution was: click on tracks menu (close track window). Click again (open it). Then it comes ok visible.
Same as this bug:
http://fold.it/portal/node/996132
See also http://fold.it/portal/node/996470
The ghost window problem seems to occur when something messes up the "h" (height) keyword for a particular dialog in options.txt. For example, "behavior_options/h" : "88" causes the behavior options dialog to be folded over itself.
I've made this happen for behavior and view options on a fresh install.
A workaround is to close the client, update the "h" keyword with healthy values, and restart the client.