Automatic dropdown command might be the problem. Try deataching collier and then command it "join&load ordnance". It should work.
Just did the following and still no dice.
-Perform "Detach Colliers" with the main fleet at a waypoint.
-Set the detached colliers to "No Auto Ordnance" on the dropdown menu.
-Perform "Join and Add Ordnance to Fleet" to rejoin the colliers.
After these steps, the dropdown for the re-attached colliers reads "Load Fleet Ordnance. " However I still see no transfer taking place after several hours. Some other details that may or may not be relevant:
-I initially had shields up and sensors on, for the target ships. Turning all that off didn't fix it though.
-I'm in a combat situation; there's an NPR in mutual sensor contact and they've been shooting missiles at me.
-These colliers are also tankers. Fuel transfer appears to work when I set the proper command on that dropdown.
Edit: Is there something I'm supposed to do with the loadout template of the colliers themselves?