I have the 2010 Laramie Crew Cab and have the rail caps. All I can say is that without the shims it leaked and with the shims it don't. Hence my suggestion to use shims. The shims also make the cover fit tighter between the rails.

 

Mine has rail caps and has leaks, bak sent new rails and still leaks but I still do not have the shims installed, getting ready to redue the side and tailgate seals and I am going to install the shims, I have about 1/4" gap, also I think people received the shims but don't realize it at the time, I had a long piece of foam that was the shims but the instructions did not indicate that this is what it was for. My only other problem is the side rubber gets torn up by the cover in the up position or folded up flat all the way towards the cab, gonna smooth the edges of the the bak in those areas after replacing the rubber, looks like a job, let you know how it goes, Bak sent all the stuff needed to do the job.