I had, actually am having the same issue.
I have a wired, roofed, sealed with buried 12" deep hardware cloth and have seen and caught rats within it at night.
I have a sand base of about 8 inches, and they are tunneling under it. and building dens within the run it self, under the waterer, under the roosting logs, under anything, actually under the timbers the run is built off of.
My solution is to set rat traps....looks like your normal mouse trap but all grown up. When the ladies get locked up at night in the coop (which has not been invaded to my knowledge) I set out 6-8 traps in my run that is bout 20 x 10.
The only thing is when I let the girls out in the morning, I have to trip, and pick up all the traps, and set them back out the next night.
Check for soft spots in your run, may be tunnels, and they might not be coming in, they may already be home.
Good luck
TNT