most likely your top mechanism is out of alignment. this happens sometimes with wear and tear and the process to get it back is pretty straight forward and requires about 30 minutes of your time.
read this article and see the last section regarding the alignment of the top:
Porsche Boxster Convertible Top Repair - 986 / 987 (1997-08) - Pelican Parts Technical Article
i dont recommend the power drill method to spin the cables but rather just unplug one side at a time in the top motor otherwise you risk stripping the threads on the cable and then you have a new problem.
another reason could be that the nylon gears in the top transmissions (one on each side) are worn and the mechanism doesnt have the power to pull the clamshell all the way down. when you hear those final 2 seconds of the top operation (when opening) that's when it's tightening everything down. broken or worn gear teeth in the transmissions might keep the mechanism from closing it all the way down.
i suggest first trying to align it and if that doesnt do it open the transmissions up and see how the gears look like. it's a bit of a pain but not too hard and you can either buy used transmission replacements or buy aftermarket gears that are not made out of nylon.
mine was sitting too high on one side and simply aligning it did the trick!
i subscribed to this thread so if you guys need additional help with it let me know. you can also PM me.
good luck!
Cristian