Thanks James, I think I figured out my issue. For some reason the Dini I am using sometimes doesn't record changes from NORMAL rod to INVERTED rod when measuring intermediate sites during line leveling.
I had to manually edit my DAT file to include 'TO Normal rod' lines where they were missing in the RAW DAT file from the Dini.

Is there a specific order I should be selecting 'Intermediate Sites' and 'Inverted Rod' in the Dini when I a leveling? I am thinking maybe I should update the firmware of the unit.
Any ideas of what is going on?
Thanks.