Just had the same problem tonight, and you helped fixed it for me.

The problem with mine was that my backpack was so large that when it was full, even with the weight reduction, I was slightly encumbered. My autoloot settings were set to stop looting when encumbered, so it would stop.

I fixed it by inhibiting every container except my key ring and backpack, and setting weight to unlimited. Started filling the backpack up again.