I fixed the dissapearing Rubat crystal!
HAHAHAHAHA! This was driving me nuts because the one thing I don't want bugged in a Jedi game is my lightsaber, and I spent hours trying to figure it out.
Basically, I built sabers with every crystal and saved/reloaded/took apart/put back together/saved/reloded...... and discoverd the only crystal that really seems to have a problem is the Rubat.
So after much mucking around with everything Rubat related; I inserted a blank entry above the very first line of upgrade.2da and numbered it 999 (just to make is useless and not get in the way of anything), And viola! no more dissaperaing/stacking Rubat crystal.
I'm not sure why this works, but I can confirm that any crystal (don't know if this will happen with other upgrade types as well) in the very first line of upgrade.2da will dissapear after transitioning to a new area or saving and reloading.
Anyhow, you can test this but using an umodified upgrade.2da; upgrade a saber with a rubat crystal; save and reload, it's gone (but effects stil there until you change color crystal). Then use the fix I've described to do the same thing, and the crystal will be there.
Hope this makes sense... I'm a little screwy after all the time I spent on this. Maybe I'll figure out how to use the patcher tool to make a fix.