When I loaded your workspace, I believe the Blind/Buried Drill files may not have been set up correctly. For example both Blind/Buried drill layers "nc_drill_BLIND_L1-L10.drl" "nc_drill_BLIND_L11-L20.drl", did not have the correct layers associated with them. I went to the menu: Setup | Blind/Buried..., and assigned metal layers 1-10 (for the first drill), and layers 11-20 (for the second drill file).
Once I did that there was No Net Compare Errors when I ran the check. See my quick tutorial movie below: