That's odd then... hmm.

Check whether you've got -df in there by finding the foldit.bat file (it's in the same folder), right-clicking it, and hitting Edit. If Edit is even a choice, that is -- but it should be. If it isn't, then open up Notepad some other way, and then File->Open, and browse to the batch file (you'll have to change the File Type thingy to "all files").

The bottom line will look like ".\foldtrajlite.exe -f protein -n native" and that will be followed by some other arguments (though the .exe on the end of foldtrajlite may not be there -- but I believe it will be). Check whether -df is among the other arguments, and if not, add it (they're just space-separated), save, exit, and restart the client.

-df makes it be able to buffer more than 6 result sets at a time. If you don't have -df and it gets to 6 sets but still can't upload them for whatever reason, it'll just exit.