Seems like the last ones I bought from TRF had the longer thread, but that was a few years ago and I'm not certain.
There is an easy fix for the wood, though. Take a wooden matchstick, coat the end with wood glue (Elmer's will do in a pinch) and stick it into the hole as far as it will go. Break it off flush with the surface, then screw the peg in. If you want, you can leave it not quite seated until the glue sets, but I generally just go ahead and put it all the way in. Give it some time before you put a strain on the peg, though.
For larger holes (like where the screws for the side curtain mounts go into the doors), I use a hardwood dowel and drill a hole to suit the dowel. The resulting repair is stronger than the original wood.