I think I had something similar recently whilst messing with some editor scripts. Pretty sure I had the same or similar message, but it disappeared after re-opening Unity.
However later I noticed a persistent tiny 16x16 pixel window in the top left of the desktop. It couldn't be selected, closed or anything. I tried looking for some Unity cfg/preferences for editor windows to remove it, but didn't find anything.
In the end I tried re-setting the editor layout (top right of editor) to default and that got rid of it. Might be worth a try.
Of course you should also check that you don't have any bugged editor scripts or 'failed to load' editor tabs around, i.e. anything else that may be related to the error.
Failing that one place I didn't look (on Windows) was the registry to see if Unity stores its editor windows in there. Assuming you are using Windows, it might be worth a rummage, before the final solution of re-installing Unity.
