At various times, both the keyfobs and the keyless entry refuse to work. The batteries should be fine on all controllers - so I'm at a loss with what could be going wrong with the rig itself. Any thoughts?
I can't speak for the Ford system but on my Jeep when the FOB starts acting up it is because the battery is low. Unless you just replaced the batteries I would try putting in a new battery in one of them and see if the problem persits before tearing into the van.
While Randy (from IA Solutions who installs the alarms and keyless entry systems for SMB) has more knowledge in this area, I will tell you that sometimes just being parked in a certain area affects the operation of these systems. I can't tell you how many times we would pull a new SMB to the front of the SW factory ready for the new customer to drive away, when we could not get the keyfob to work. We could pull the van forward a hundred feet or so and all would work great. Go figure!
You might want to confirm if the problem occurs at the same location(s) only.
When it acts up try putting the transmitter part against the skin under your chin and key up the entry and see if it works . I have done this numerous times with different vehicles and always amazed me . Being simple has it's virtue's , sometimes for fun I start pushing the lock button as I move to and from the vehicle just to test the range and always find that the contact with my chin increases the distance for activation .