Not really sure this counts as an actual answer, but, nonetheless...
Something similar happened to me with
pset3. When in "CS50 Submit" page, I clicked "upload", selected the file, "OK", commented the version... So far so good... But, when clicked on "Start Upload", the page would just hang...
So, couldn't help it, I'd click "Start Upload" again... < blank >... and again < blank >... Eventually, I decided to wait a couple more seconds, and it actually submitted. Problem was it submitted one correct submission (the first one), followed by several empty submisions, that would "take precedence" (regarding grades) over my proper one.
If this is your case, you should just wait till it actually "digests" your submission, in order to avoid empty submissions.
P.S.: I'm using Firefox 33.1, BTW. Don't know if the "lagging" button could be exclusive to some browsers ;)