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I used the Runtime file, the SA+SO objectives, and the Offline Elusive targets compatibility SA+SO. 

I even made sure that the file for the elusive targets (chunk0patch59.rpkg) was below the offline scoring mod (renamed to chunk0patch49.rpkg). The problem still persists.

Works for me with the same patch files, so this seems to be an issue on your end. Maybe try uninstalling all other mods or verifying game files and installing mods again?