A known problem on 4runners as well. Owners there either remove them (not sure what function they serve) or put a dab of clear silicone on them at each end to keep them snug but removable ...
I never put mine back in after the rack went on. I figured it would not hold onto the moisture. It was pretty dirty under mine, now it gets washed out with the rest of the truck.
I saw this thread a few days back and found it funny how someone would worry about a small rubber strip and was going to say just chuck them out they're useless.
guess what happened right after I left the car wash today?
It flew off the pasenger side and got wedged over the drivers side.