It should be pumping anytime in gear or even in park. Was it sitting with the front end up in the air for awhile? Could be some drain back.
To check your flow pull the lines off and direct them in a pan with some hose. Have a buddy start the car for a quick second or two. Watch the flow.
It should shoot out pretty fast. Be carfull.
I know on the late model Mopars it only pumps through the cooler in gear.
Did alot of trans flushes when I was still at the repair shops.