Strange... I had a quick look through some old NG maintenance and training manuals and couldn't find any inputs from the flaps into the autospeedbrake system.
Are there any other aircraft configuration changes involved in a flaps up landing?
Is there anything on your aircraft which stops you moving the speedbrake lever to UP in flight? (I thought the NG had no electromechanical lock, just a notch to let you know you'd reached the flight detent)