Just my own personal observations.
It doesnt seem to happen to me while "running" a ROM, it mainly happens while flashing OR just after flashing anew ROM(it hasn't mattered which ROM). I did notice that(I just lost the symbol again
) I did a factory reset, and upgraded ROM's yesterday, and I noticed that when it was restoring My Playstore Apps, the battery got REALLY hot. I've noticed this on 3 or 4 different occasions after upgrading, the battery got hotter-n-hell, and the GPS symbol was later gone. Now, I dont use the GPS a whole lot, so I dont see it's gone right away, but those are just what I'm thinking.
Just re-flashed back to stock LEM, did your magic trick to get GPS back and have updated to a custom ROM, so we'll see what happens next