A bit of background: Today I was doing the Battle for Kvatch quest and after I left Kvatch, wherever I fast traveled I would still be stuck in a thunderstorm (not the Oblivion weather, just a normal storm). I have the Steam GOTY version.

Full list of mods here:http://tinypic.com/view.php?pic=20szp5h&s=8#.U9P2uvldV8E

Along with Darnified UI, Qarl's textures, RAEVWD and Natural Faces.

So in order to try and fix this I went into Wrye Bash to rebuild my Bashed Patch and to resolve any conflicts. I rebuilt the patch but it turned red, so I examined the conflicts. All Natural Base.esm was conflicting with the Unofficial Oblivion Patch, and some components of Natural Environments (not the Weather) were conflicting too. I redated the timestamp on each one to turn the mods green once more. I also saw that there was a delinquent master error for my Unofficial Knights of the Nine patch, specifically the Knights.esp., which I ignored. After that I ran BOSS and rebuilt the patch. This time I took a look at the Masters sidebar on the right of the Wrye Bash window. I do not have any of the DLC, but the patch apparently included the Spell Tomes and Frostcrag Spire DLC which were highlighted in red. So I went into the Update Bashed Patch window, and deselected anything to do with the DLC, retaining items relevant to Shivering Isles, KOTN and Oblivion itself. After I did so, the Bashed Patch turned green. I launched Oblivion, thinking I had solved the problem, but then it CTD.

Also my Bashed Patch will not go to the end of my load order despite multiple attempts using BOSS.