Ah, I do have TTRSO loaded earlier in the list; it's probably that. I'm tempted to give Ordinator a go though too. It looks like there could be some good stuff in there.
One thing I wasn't too sure about is how LOOT handles modified/merged plugins. I've used BOSS until recently so I'm still getting to grips with LOOT. With BOSS, it obviously wouldn't recognise any non-standard esp names so you'd make your own load order rules in those situations. I've yet to see LOOT highlight any unrecognised plugins... is there still need for some manual intervention beyond the mods highlighted in the packs?
Edited by Quinnbeast, 24 August 2015 - 08:05 AM.