I had a similar problem and found that the teeth simply backed out. I used a small needle nose and pulled the teeth back out and made sure I had the zipper end set properly then zipped and in zipped a couple times and it set the teeth back in place.

 

Find an upholstery shop that does vinyl boat covers and tops - they should be able to sew in a new zipper for a lot less than the cost of a new top. I've got a few teeth missing in one of my zippers, but I can still open and close it so it hasn't bothered me enough to look into it yet. I'll go that route first if it ever comes to that.

 

Does anyone know what bottom part of the zipper is called? The part that holds the two sides together while you zip it up? Mine fell off and I need to buy a replacement and crimp it on... Will never take my window out again... UGH