Okay, I found the event, actually 1 of 2 events, depending on when the scenario starts. If the scenario starts before 1863, evt_nam_USA_ChasseursAfrique1862 gives you the 1st LA 'Chasseur d'Afrique' unit and puts 30 so-called Colored Militia in your unit pool. If the scenario starts after 1/1/1863 evt_nam_USA_ChasseursAfrique_Post1862Scenarios fires and just gives you the 30 so-called Colored Militia in your unit pool.
The Colored Militia are however actually volunteers and basically the same as non-colored volunteers.
The problem arises because the Colored 'Militia' volunteer models upgrade to the same model as the non-colored volunteers. This I think is an oversight, because there is a line infantry model they could upgrade to for "Black Troops". Why it wasn't used I have no idea. Oversight is my guess.
If you mod the 230USAVolunteers.mdl model file changing 'TrainUpg = $mdl_USA_Inf1' to 'TrainUpg = $mdl_USA_Inf7' the "Colored Militia' will upgrade to line infantry "Black Troops" and the issue should be out of the world.