Wait, so you got it working? It still says in use, but doesnt crash, but still saves?!? Also, if I run as admin it still crashed after hitting cancel 4 times...
Are you running the exe from steamapps\common\skyrim? The Steam shortcut won't give you the option. On CreationKit.exe > Properties > Compatability > Run as admin.
And yes, it still says in use and you have to press cancel, but this time it doesn't crash at the end. Maybe make sure Steam is running as admin too.
EDIT: I just tested without admin and it doesn't crash at the end anymore either. Uh oh...But that was the only change I've made since the crash.
My WS is a new one with values pasted from Tamriel except with HD LOD Diffuse/Normal empty.