Make sure you aren't confusing a checked mod in the left hand pane with a loaded *.esp in your load order. This is not actually what that means.
Esp/esm files are activated and sorted in the right-hand pane and LOOT will show those results correctly and they will correlate with what MO has shown, and vice versa.
The left-hand pane is showing which MODS are loaded. Note I said "mod" not "esp". Mods, as you are aware, contain resources like meshes, textures, menus, etc. When a MOD is checked in the right-hand pane it is merely showing those resources are available for use in the game.
So you may have installed a mod that is only providing textures, like the Hi-Res DLC, that doesn't need an esp to be used. That means it is unchecked in the right-hand pane but checked in left-hand pane.
The mods you bashed probably still provided resources to be useful and they will still need to made available, ie checked, in the left-hand pane.