I can't say because I use clear packing tape. I put a piece on both sides. It works great and sticks well. It is also not very noticeable.
The light on sounds like a good conclusion. I would say the slides could be to blame too. Pulling or pushing out the slides while the top is too low, or even a jagged edge on the slide where the window could catch when in stored condition. I have a few holes in my windows and can only theorize these are the reasons the holes are there. My windows are getting crunchy and very yellow though.
I'm not sure if it would work, and if it has been mentioned before and shot down, forgive me...I don't know what type of vinyl they use for the windows, but would a waterbed patch kit work? If it will make a waterproof patch on a waterbed bladder, could it work on the window vinyl?
Like I said, not sure what type of stuff they use for the clear windows, but it may work. Also, if the material in the patch kit is not see-through, you might try using material from a clear vinyl shower curtain or purchase a small piece of clear vinyl from a craft and fabric store like Joann's or Hobby Lobby and the glue from the kit. Try it on a piece of scrap to make sure it won't cause more damage...it's worth a shot.