A fellow player named Bridger4 reported me in mod.io that part of Paid Wages wasn't working in a modded game. The mod game in question did not alter that part of Paid Wages, so I went to investigate further. Turns out that the "+20 stability on captured cities" effect on that civic is NOT working. I fiddled with the modtools and managed to fix the bug, by changing the descriptor on Effect_Civics_Army03_Choice01 from Empire.Cities with GameEffect_CityFlags_Captured validation to Empire.CapturedCities. This imgur link shows the bugfixing mod in action and the descriptor changes needed to fix the bug.

To reproduce the bug, simply fire up a game, get the Army Wages civic (be at war, control 10 units), enact the Paid Wages option and capture a city. You'll notice the stability on captured cities not working (the +5 stability on garrison part works fine).