I'd guess then that the holes were poorly drilled then (on the hugger that is). Could you widen them enough to get them to line up and then use trim plugs with bigger heads or washers to cover the enlarged hole?
The trim plugs I use to hold the flap on are these...
http://www.ebay.co.uk/bhp/plastic-car-trim-clips
There are others available with wider heads too. Cheap and cheerful and in bags of 25, so you can aways carry spares.
I got sick of fiddling about breaking the OE ones, losing the centres in the swingarm, plus the originals don't like mud and grit.