Update on mine: so its clear I'm running +5 offset wheels with 285/75/16 BFG muds and a 50mm dobinsons lift.
I did the panel beating on the weekend and then put the front arch mud flap back on and it scrubbed still
So much in fact that when I went to park it and pull it back off I ripped it off the mount :x
I was very pissed off at the time but I can see that the stock mud flaps are unnecessarily too thick so I'm going to get some sheet rolled and pressed to do the job (i.e stop mud spraying up the side of the car).
It seems that my problem is the offset of the wheels combined with my larger tyres but I can still get around it and I like them so I'm sticking it out.
p.s if you take the liners off take close note of which plugs, screws and bolts go where or it'll be a task putting them back on. Was for me at least since I took them off about 3 months back and it took me about 3 hours to put them back on with the wheels of though I did stop and start a little.