Hm, not sure this is really a good try on a new load ordering unless there are a few things no one said so far.

After the update i did reorder the list with the launcher tool (boy that was not funny), trying to start Skyrim and instant CTD. looking at th mod list in WryeSmash shows that both "Skyrim.esm" and "Update.esm" are disabled.
Manually enableing them and running Skyrim it works, well point is if i now get back to the launcher tool to check on the load order it got completely reset, back to alphabetical ordering, making changes again disables Skyrim.esm and Update.esm again.

so whats the catch with this?

And where does Skyrim now store the load order? couldn't find any file that contained any ordering info.

same problems here...

also when i deleted a mod, my load order reseted back to alphabetical order, just [censored].

Okay the file does exists now, (wasn't present in %LOCALAPPDATA%\Skyrim before, but after around 10 tries to edit the load order with the launcher tool, it suddenly appeared)

From the other thread about this change, does anyone know if it is possible to edit this file manually and have the changes stick? and should the Skyrim.esm and udate.esm be included in this file?
ATM i tried that, it works, just not sure if that is a good way to go about it.

Head on over to the mod forum for all your answers.