"What could have happened" is indeed a question for discussion but on the assumption that you actually want to cure this I have moved it to the Support forum.
One possibility is that for some reason there is a failure for your board to "phone home" for the version check.
Some hosts put a block on such connections and if yours has done so then there could be quite a time elapse between the attempt and the point it would normally come up with the "could not connect" error
One way you could test this would be to open the file templates/yourstyle/admin/index_body.tpl in a text editor and after making a backup remove the call for the version check
The truth is out there.
Unfortunately they will not let you anywhere near it!