well i checked the ACU upgrade function, but the Experimetal Wars version here (v1.87) has no change in ACU enhancements
and works well with Black Ops.
This version (v1.87) is based on the original version V1.8 and i guess you are playing version 2.8.3 ?
As far as i can remember, Experimental Wars V2.8.2 (one version earlier) has no commander upgrade change.
So V2.8.2 could work with Black Ops.
Sorry that i can't help more.
Test: ExpWars 1.87 and Black Ops: