IME they can need a fair bit of tinkering with to get them just right.
The last ones I had I needed to leave a roll of insulation tape wedged under the edge of the front one when it was in the shed, to train it to sit away from the tyre.
There is an excellent install video on the Crud website that's worth watching too.
Sorry but I can't link to it from work.
Agree - it's better to spend a couple of hours fitting them, rather than constantly tinkering around with them.
One trick is to make sure that the cable ties are loose. Also, if you're not aware, there's a fair bit of movement allowed at the screws where the stays attach to the mudguard.
You could also shave down the brushes as this will often cause the rubbing.
If the mudguards are only just catching then they should settle down after a while.
On my Boardman I actually didn't bother attaching the front part of the front mudguard (Mk1's) as it doesn't do that much anyway.
I think Cruds have their place, but I decided to use a sledgehammer to crack the nut and just bought another bike that had proper mudguard clearances in the end. They [the cruds] just got on my wick too much (very flimsy-was always nervous of touching them as they would often go out of kilter).