I figured out what you guys ment when I went to clean up an assimilated Constitution.  it was based on Anduril's connie, and uses an animation effect on the bussards.  the motion ripple behind swaps three 10% transparency bussard caps to create the motion (like what, if I remember right Baz was having trouble with on one of his nacelles).  trying to create a new ripple effect (to be more Borgish) without redoing the original caps resulted in the motion cap overwriting the glow cap.  this is why I think most of this involves levels of transparency that can be set in Photoshop.
what it shows me (and anyone using a program like Irfanview to view "loose" skins) is the non-masked areas of the glows, and nothing else on the skin.  again, when I view masks with my program, the glows are there, at about 50% transparency.  the rest of the skin is replaced by the patterns that indicate "transparancy"  I'll have to post a pic that shows what these skins look like in Paintshop
btw, keep away from those IED's, markyd, and good luck.