Nah, everything checks out in the initial status. The funny thing was, I placed a new model (so that it had a new model # in FRED), deleted the old one, and renamed the new into the old. Came up with missing glows again, which leads me to believe that something in the file is tagged to the name.
It's Steve-O's frigate, and it's fine otherwise in every other mission I put it in.
Aha! Just pinned it down. Ships that arrive later into the mission (ie. those who aren't there intially at the start of the mission) lose their engine glows. With and without warp effect. This also applies to fighters and small craft as well. Interestingly enough, it only seems to apply to that particular mission.