I'm not sure how to explain it. My Skyrim MO works fine when switching between profiles, and uses similar programs in much the same way (CK vs GECK, TESVEdit vs FNVEdit, etc) so I don't think it's a matter of being installed incorrectly.
I have four profiles: my main profile plus two copies of it - one a backup, and one for tinkering around without affecting the main profile. I haven't used either in a while. Then I have fourth profile of very basic mods to test mods on a low load order. Whenever I switch to my basic load order profile and launch the game, the GECK, or FNVEdit, the load order on my main profile becomes disorganized. It's solved easily by just copying the loadorder.txt from my main profile between switching, and then copying it back in when I'm done. Still, it's another step that shouldn't be necessary. I organize my load order by hand, since it seems that no auto-sorter understands how to sort Tale of Two Wastelands or FOOK-PN Convergence, and they turn my load order into a mess. So it can't be that, either.
I'm not expecting any changes I make on a profile to carry over to another profile, that obviously defeats the entire purpose of profiles. Yet for some reason using one profile messes up the load order of the other, but it was my understanding that MO is supposed to keep everything isolated. So why would launching an executable in one profile change the load order of another? It's not a huge problem since I can copy the loadorder.txt, but I'd still be thankful on any suggestions for why this happens.
Edited by Sarcasm, 03 February 2015 - 07:19 PM.