When hitglows' colors are defined as "same as fret" in the theme.ini, the hitglows appear to use hard-coded color values, as opposed to the defined fret colors as evidenced by the fact that 5th fret hitglows remain orange despite the fret color being changed to fuchsia. This bug's been around for a while, and I have noticed it before. I couldn't find an issue for it though.

it also uses the glow image from /data rather than /data/themes/theme

This seems to have disappeared with blazin's latest Theme changes. Hitflames appear to remain hardcoded though.

I just pushed an update related to hitglow/flame settings. http://github.com/stump/fofix/commit/90a27b5d344f24f4ea9a54b7eff146b3b04f2445

You can now completely disable hitflames as well as set them to the default glow color. I've also fixed the glow.png code so it will use the theme's version if available.

Unfortunately, setting individual hitflame colors (based on fret colors) was too convoluted for me to fix.. maybe someone else can take a look.