It's probably twisted. Do you have a swivel between the anchor and the chain? That can help eliminate any twist and also serve as a way to help untwist the line.
I do know of a friend with a windlass who uses it often who often sets another anchor off the bow once a season or so (dependent on use) and unhooks the main anchor off the windlass and lets the rode out into the current to untwist.
I used to have the same problem. When dropping the anchor, the rode would jam up and I would have to try to acces the knot from the anchor locker door in the cabin - major pain. I read somewhere that the vertical style windlass imparts a twist to the rope and if the drop into the anchor locker is not sufficient, can cause this kinking problem. When I replaced the windlass, I went with the horizontal Maxwell. I also replaced the anchor line with 300' of 1/2" eight plait style line. While this line is somewhat expensive, it is very limp and takes up much less space in the locker. Never had a jam since.