The below also applies to LOOT.

So I've run into a problem with SkyProccers before, because in at least some of them, the "Don't run BOSS" checkbox is nonfunctional.

Unless you're running your proccer with the -noboss parameter, Im pretty sure I know what the issue is.

Basically, even if you lock your load order, the SkyProccer will run BOSS and change your load order only while it's running and then your load order will change back immediately with no indication of what happened, or why you got the error.

So if you're running BOSS and then manually sorting a few mods BOSS isn't recognizing into the proper order, that's the problem. Because when the SkyProccer runs BOSS, it'll throw those mods back to the bottom of the list and then have errors with your bashed patch because of missing masters.

What you need to do is run the BOSSGUI.exe in the boss directory, and set up User Rules to sort the mods BOSS doesn't recognize into the order you desire. If you're using multiple proccers like me (ASIS, Lootification, Automatic Variants, NPC Enchant Fix, etc) you should set up rules so they are always sorted in the same order too.

Basically, if you have to manually sort any file, it's probably going to screw up. You need to set up BOSS user rules, and be using the Latest Version of BOSS.

In my experience, this is most often an issue with compatibility patches and new mods, as BOSS often doesn't recognize them.