... yeah so no... I also have this problem on regular ubuntu. I managed to make it happen on chrome and Opera and firefox (couldn't get that shot though).
I really am sure my chrome themes have nothing to do with anything like this. Besides I change them all the time. Keep in mind I have pretty much the same stuff on the desktop and this never happens on there, ever.
For some reason on FIrefox I couldn't "make" it happen just by ctrl + a it happened... less often and not normally.
Note if I do 'ctrl + a' a second or greater time the box won't pop up.
I have 263 items installed.