So far I always had set random civ as defaut. I noticed it when Austria was set instead default after playing couple of turns during CSL marriage playtesting.
I tested again with my saved game and with a new game and don't see it. I have it set to load after (6A). I checked Steam original meaningful colors, the only add was XML, no DDS files.
So the problem is occuring somewhere within either Colors.xml, MinorCivs.xml or PlayerColors.xml. The merger has 2 different kinds of XML entries. So, would that make any difference or possibly clash? If so, for uniformity, I can change all of them to one standard. One uses <Row> </Row> for entries, the other uses UPDATE, SET and WHERE.
You said you tried with ONLY VP+MC. I am still using version 4 without the added compatiblity for UCS that was put in version 5+6. What difference is there in it?
MC MOD [original] : PlayerColors.xml
RCI MOD[original] : PlayerColors.xml
MC MOD[original] : MinorCivs.xml