I've got the corrected data and am looking at it now.

I think what you are seeing is due to the intersection of 2 functions in AFNI.

1. The overlay is at a lower resolution than the underlay, so it is resampled to match to underlay grid for display.
2. The default resampling method is Linear interpolation.

Your overlay data isn't some value that is more-or-less continuous in space (such as a beta weight or t-statistic), where linear interpolation makes sense. It is a discrete value, and so interpolation between 2 and 3 to get (say) 2.5 makes no sense.

You can turn off this linear interpolation. Click on Define Datamode and you will see two controls, OLay Resam mode and Stat Resam mode. Change both of these to NN and your overlay image will suddenly go from smooth to blocky.

This switch of texture, from smooth to blocky, is very visible if you zoom in on the region of interest, but it is apparent even with no zooming.

How did I find this? I did something "tricky" or "hidden" in the AFNI GUI, that few people know about. I put the Overlay in as the Underlay temporarily (using the "U]" key into the image viewer). Then I opened the Disp control in the viewer, and chose RowGraphs to be 1. This shows a graph of the data in the underlay image underneath the row where the image crosshairs are. It was obvious then that some intermediate values were being created by interpolation.