I found the problem. It's with the Skyrim.ini. BethINI isn't apparently aware that it's SE, so it's changing this section:
sResourceArchiveList2=Skyrim - Voices_en0.bsa, Skyrim - Textures0.bsa, Skyrim - Textures1.bsa, Skyrim - Textures2.bsa, Skyrim - Textures3.bsa, Skyrim - Textures4.bsa, Skyrim - Textures5.bsa, Skyrim - Textures6.bsa, Skyrim - Textures7.bsa, Skyrim - Textures8.bsa, Skyrim - Patch.bsa
sResourceArchiveList=Skyrim - Misc.bsa, Skyrim - Shaders.bsa, Skyrim - Interface.bsa, Skyrim - Animations.bsa, Skyrim - Meshes0.bsa, Skyrim - Meshes1.bsa, Skyrim - Sounds.bsa to this:
sResourceArchiveList=Skyrim - Misc.bsa, Skyrim - Shaders.bsa, Skyrim - Textures.bsa, Skyrim - Interface.bsa, Skyrim - Animations.bsa, Skyrim - Meshes.bsa, Skyrim - Sounds.bsa
sResourceArchiveList2=Skyrim - Voices.bsa, Skyrim - VoicesExtra.bsa Revert to the first list and voila. EDIT: I should say that this is what's causing the CTD. Now hunting for the error in SkyrimPrefs.ini that causes the launcher to re-setup every time.