When that happens to me, I cheat.. I grab a glow file that I know does work, and copy it to the model directory using the same .gf name as the one that doesn't. Then I open the ship in the Glowtool, make sure that the glows are all there, clear all groups, reglow, and save. Then recache. That seems to work for me everytime.
To create all new original .gf's, I also go old school.. command prompt in the directory and then type:
echo > glowfile.gf
And then load it. Haven't had many problems that way, but if I do, again, I use method #1..