Hello jcw265, welcome to the forum.
You mentioned that you have had this problem only when the hopper is very low. Does your hopper lid have vents or screens in it or is it solid metal? Are you keeping the lid in place on the hopper??
The only way coal will burn is with a supply of air. So if it is burning further up the grate toward the hopper than it should, there has to be air supplying the fire up there. So if you have very little coal and the lid removed or a lid with screens in it, then the chimney will pull air through the hopper and fresh coal the the fire will burn 'uphill' into the hopper.
I would suggest keeping the hopper full. and the lid on.
Borrow the Manometer in the Manometer loaner program, just PM member Matthaus with your address. I'll find the link to the program thread. Here it is: Manometer Loaner Program
As mentioned if the grate is not properly sealed at the top there will be air at the gap to support a fire, but since this only happens with a low hopper, it indicates that the air is getting through the remaining coal in the hopper, so keep it full and keep the lid on the hopper.
You don't want to burn bituminous coal in your boiler. Use anthracite coal only too many problems with trying to get Ohio, West Virginia, Maryland and Kentucky coal to burn in a stoker. The stoker was designed to burn anthracite only. I've tried bituminous in a bed type stoker like yours, didn't work.
Hope this helps. Greg L