i fought this for a few years actually. the question is where are you seeing water coming in? if it's coming down the inside of the 'ring' that goes around the skylight, then the only way it can get in is from around the skylight itself. the bow pad would leak down through the ceiling.
i agree that you shouldn't reseal with the regular caulk. i did mine twice, and had various shops do them probably 4 times, all with 3M 4000 based on TAGs advice. the seal would never last more than a month...usually just 2 weeks or so.
i finally found a company that came highly recommended, and when i described my situation to them, they said that 4000 while UV stable wouldn't bond well to the acrylic. they came in and dug out all of the old caulk/4000, and then sealed with Silpruf. took them a day to dig it all out, and a day to seal it up. it's been 4 months since they did the repair, and i haven't had a single issue since.
according to this company, the original install using 4000 works because they actually bed the skylight into the bead, which allows it to seal better. since we're dealing with a repair, it just won't hold up.
i have the original install instructions from TAG if you're interested.
good luck
twarble