If You have only torpedo core and flares showed up but no torpedo glow but only square so You have wrong torpedo glow map name, You have to go to scripts/tactical/projectiles and there search for torpedo plugin you want to edit then open it in notepad and find those lines pTorp.CreateTorpedoModel(
"data/Textures/Tactical/qCore.tga",
kCoreColor,
0.6,
3.5,
"data/textures/tactical/qGlow.tga",
kGlowColor,
7,
7.10,
7.75,
"data/textures/tactical/qBlank.tga",
kGlowColor,
0,
0.1,
0.14)
and check paths to those tgas if they fit with tgas in those directories if something is different it causes problem.