Up until this latest release of LOOT a day or so ago, Vortex and LOOT didn't seem to see each others user rules and possibly the master list. I got such strange behavior that I stopped using LOOT altogether. Upon loading this recent version of LOOT yesterday, all of the user rules I had set up in Vortex were there. People need to remember, not all plugins have a rule so their sort order isn't fixed and any change should be expected. If you want to ensure load orders, for whatever reason, use priorities. The primary reason I've had to do this was to ensure the masters for my merged plugins don't change their order.