I had this bug on Tribble at first as well, it was fixed in one of the earlier Tribble patches. After choosing a KDF alliance my Romulan's warp trails when leaving a system are now red instead of green. Ticket ID #1,683,823.
Teiberyn - Romulan (RR-KDF) Engineer - R.R.W. Viserex, Fleet D'deridex Ril'el - Romulan (RR-FED) Science - R.R.W. Pellecia, Fleet Dhelan Shephard - Human (FED) Engineer - U.S.S. Dauntless, Fleet Sovereign Rhys - Joined Trill (FED) Science - U.S.S. Palatine, Vesta-class
@Captain_Shephard - Join Date Status: Assimilated - Twitter: @RogueJawa