From my own experience, and from many others, I don't think SkyUI is that buggy. If you untick all your mods and just load the game with SkyUI only on a fresh game, does that work? Steam doesnt overwrite SKSE in anyway, especialy since using MO doesnt place the files in the steam folder like a manual install. I am using a modified STEP setup, along with a number of non STEP mods, current non beta SKSE, and have had no problems with SkyUI. I am curious now though, could you use the spoiler tag and paste your ini contents from the 'Documents/My Games/Skyrim' as well as from inside MO?