If it's only the GC mutator turning off, then it doesn't make sense.
The GFT (or was it GTF?) "fix" for NanoFXv2Beta doesn't fix anything at all, in fact, it introduces errors because it just dumps a load of systems, including the special Starbase12 and Drydock systems, and several custom starsystems that people might not have installed.
The only fix there is, if you take the definition of the word "fix" rather broadly, would be that NanoFXv2Beta (it is a beta afterall) didn't include _all_ the systems. And it (that is, the GFT fix) fails misserably at that.
It's a pity I lost both mine, and JWattsjr versions of the correct way to do this.
About the sudden exit (one ought to classify that as Crash To Desktop) is one that only happens with lots of mods installed. Actually it could be a single mod, or multiple, or the combination of multiple mods. It's annoying, but short of testing each mod, one at a time, is far too time consuming for anyone (or a team) to do, even at 16 hours a day.
There are people working on it, but not like that. For example, the BC Supermod (try not to install mods on that) doesn't have this problem.