AKA: Why do I have to mouse over (flagged enemy) players to get Class Colors to appear?
Make certain your Blizzard "Combat>Class Colors in Nameplates" option is enabled. Otherwise, a mouseover will be required to determine the class of flagged enemy players.
At this point (WoW 3.0.2+), it is strongly recommended that all Aloft users enable this Blizzard option at all times, and control nameplate display colors with Aloft. This Blizzard option will not interfere with Aloft's operation.
Also make certain your Aloft "Health Bar>Colors>Color Hostile by Class" option is enabled.
NOTE: There is no similar "inference" capability for friendly players. All friendly nameplates are colored the same by Blizzard, and Aloft must override those colors on behalf of the user. Therefore, friendly players will still require a mouseover/target action to determine their class, at which point Aloft's "Health Bar>Colors>Color Friendly by Class" option can apply class colors to friendly nameplates.