The thruster Starman is talking about -- that is in the screenshot -- is Thruster02-03, the Secondary thruster. Wanderer, your description of primary glow sounds similar to what is happening here, but this is not the primary glow. Note that the ThrusterGlow also has the 180 degree field, which also vanishes... but it's the secondary thruster, the 'trail', that is most noticable.
The problem has been around for so long that I almost forget to notice it anymore. On some ships the fading looks natural, because wings and stuff get in the way... but on others, it's silly. The Ulysseys is a decent example of the silly.