I believe this is a function of your scanner (TWAIN) software. I have a Cannon copier on my network and the software provided with it allows me to scan massive documents (1-sided, 2-sided, etc)from the feeder.
Check your interface sofware to see if there is a setting that will allow use of the feeder. It sounds like the software is only recognizing the platen (glass)and therefore asking you to place the next original either on the platen or in the feeder to be fed to it.
I know this is not the best answer but it has worked on my network.
good luck.
Aloha,
cg