In the first screenshot, I had put the <Hide Equip> note tag on the "Attack" skill.
And for some reason, it still shows up in the skill equip menu.
Though I admit, this could be the cause of plugin conflicts - I'm not too sure.
Unfortunately, I'm having the same issues and moving the plugin to the bottom didn't work. My issues are that "Hide Equip" doesn't hide the Skill and if a Skill has "Always Active" I can toggle it on and off even though it stays the color Red.
Love the plugin overall, but any help with the issues would be much appreciated!