bad move ... the more little sealed areas you have, then the more areas for water/damp to get trapped,
best thing you can do is the following ....
1) never screw them into the box section or arch (causes water to get in)
2) dont try and seal the gap, but make it bigger !!
here is what i did ...
1) repair the knackered sections !
2) get 4 nuts and bolts (about 2 inches long)
3) get 4 valve step seals, top hat ones (i think mine came from a vauxhall)
4) weld the bolts head first to the box section in the reqired places, creating studs
5) slide the valve seals on (narrow end first)
6) fit mudflap and fix in place with the nuts
this will increase the gap around the back of the mudflaps, it will not decrease its efficiency much and will allow the mud/water to come out easier ... and when you wash it the hose will flush all the crap out nice and easy
this i did on a mk2 ... but should be fine on a mk3 if you dont mind seeing the small gap