Can you check if you turned "Smart Player Colors" on at some time?
"Smart player colors" option is indeed on; it would've been on since the start of the game though, as I fiddled with the options before starting a new game and left them untouched since. The colours were fine at the start but changed at some point, possibly after loading a savegame.
Unchecking the offending option and reloading the savegame restored original colours for me, so the change isn't permanent.
