NOTE: I'm responding to you as if you might not know how to do everything correctly with MO2 as I can't read your mind to check whether it's true or not. I don't believe that you would be misleading intentionally, but you might possibly be mistaken or groggy etc. I always have to check now due to previous experiences helping people on the skyrimmods discord.
None of your mods in the left pane are enabled. Click the check boxes on the left, or select all of the disabled mods, right click them, and click "enable selected". This could cause your difficulty persistence issue.
Your engine fixes mod has a warning icon on it, you need to mouseover that warning and see what it says, and correct it. If it's not updated correctly for your version, this would also cause the difficulty persistence issue.
You also have a warning symbol above the right pane, you should check that out as well.
The left pane has its own priority system for the loose files - scripts, textures, etc. The right pane with the "Plugins" tab selected has a plugin (esp, esl, etc) priority. You adjust this priority system using LOOT to sort them; you can add loot to MO2 and launch it as an executable from inside MO2; unless they've changed this, the version of LOOT that MO2 has built-in isn't in date or doesn't have an up-to-date masterlist or something, so you want to actually download LOOT separately, add it as an executable, and run the executable using the drop down list above the left pane or add a shortcut button to it in MO2.
If you need further help, you may need to look up guides for MO2, as I only look at the nexusmods forums like 2 or 3 times a year and I probably won't remember to check for replies.