@engikeneer That did the trick!
You can even see the spot where I have a tiny piece of plastic debris stuck under the flex plate in the height map 
I've got the stretched spot over where it won't cause any harm until my new roll of belt material gets here.
Thanks for the insights!
@engikeneer The linear rails and frame pieces are far too heavy for the printer to be able to bend them, but I think you have put me on the right track. I've been focusing on the rails, but when I ran the belt past the spot on the rail where any defect has to be, I noticed a slight increase in the drag on the belt. Looking closer at where the belt passes over the pully around that spot, I appear to have a small section where the belt has been stretched and the belt teeth don't mesh perfectly with the pully teeth. That's probably where the effector got stuck and the motor stretched the belt trying to keep going. That stretched spot (about 20-25mm worth of belt) could cause that effect similar to a missed step. Time to order some new belts and see if that fixes it.