I think you may be mistakenly interpreting the "use ratings" setting as how the CM pick lineups for games. It is not - that setting is ONLY for the intial CM-generated lineups for the CM profile. For any given game, the CM will base its lineup on the profile lineups modified by the spot percentages specified in the depth chart. If you generate a CM profile with "use ratings" the depth chart automatically sets all bench playing time percentages to zero. If you do not manually modify the sport percentages in the depth chart, the CM will use the basic lineup for every game.

So, check the spot percentages in your depth chart.