Try unchecking the Application Frame and the Application Bar from the Window menu.
That did not help. Sorry.
This happens with all the file or with new files only..
Also try resetting the preferences :-
hold Cmd-Opt-Ctrl-Shift when restarting AI on a Mac or Alt-Crtl-Shift on a PC to reset the preferences to the factory defaults
Also let us know your OS
Mac OS 10.7.3
I have reset preferences, as well as tried opening on multiple machines. This was a file created today. It is just this file I am having the issue with.
I know thiis is late, but I am also having this issue. I haven't been able to resolve it, but what works in the meantime is, when it gives me that message I say OK, then maximize the Ai window then go File, Open Recent, and what you attempted to open should be there...and it will then open.
I don't know how to get the message to stop popping up though.