Sometimes when I'm sewing with spool thread, the thread gets caught in the slit made at the bottom of the spool to keep the thread from unwinding.
i was hand trouble yesterday with freemotion my top thread was all loopy on the underneath side....I ended up having to set the top tension as high as it would go and then it worked fine.
If you are using a hopping foot, try not dropping the feed dogs. See if you can still freemotion.