So, I read in the FAQs that it means my load order is botched, but I don't see how. I'll post everything I did.
I was following this http://morroblivion.com/forums/morroblivion/mods/2173 Before I started, I had just done a clean installation of Morrowind (Including Tribunal and Bloodmoon, tested to make sure it was working) and Oblivion (with Shivering Isles/Knights, which I also tested) I installed both games in C:\games\Bethesda\(respective game name here)
So, after making sure everything was working, I got started. I installed The Unofficial Oblivion Patch, followed by OBSE, and Ely's silent voice. Then I installed morrowind_ob.esm using the installer, then the complete installation, then DARNified UI, Themed loading screen, protocolled dialogs, (and MenuQ which is required for protocolled dialogs).
I installed no other mods, and after this I opened up wyrebash, and this is my load order.
Oblivion.esm, Morrowind_ob.esm, Bashed Patch (I have no idea what this is or if it needs to be on or not), Unofficial Oblivion Patch, Shivering Isles, Knights, Morrowind_ob files, with CAT last, Loading screens, dialogs, and lastly, the Morroblivion lighthouse home.
To run the game, I always open it using OBSE. It will crash soon after I hit new game. Am I doing something wrong?

I have no idea what Bashed
I have no idea what Bashed Patch is either,but try unticking it in the OBMM as it certainly is not used by morroblivion,and if it is used by other mods you will notice which mod [if installed] is affected by it being unticked.
Try not using DARNified UI, and Themed loading screens,they might not be the reason but worth a try I quess.