I updated to the latest version.I installed it in the skyrim folder and it works there.When you install it make sure you designate the directory inside Skyrim directory.
I take it you mean to install everything inside Skyrim.I installed it from inside Skyrim but into its own directory.As for clean install I take it you mean a  complete uninstall including deleting everything left over in in the MO folder.
I have only one profile,Default.Where would you suggest I install it?Im running windows 7.Its presently installed in Program files x86.I have a 2 terabyte hard drive.The machine is new and I have 1.5 terabytes available.
I have this same problem.When I run it as administrator it gives me the same message and then crashes.This is happening ever since the 1.12 update came out. Ive already uninstalled and re installed the program 4 times since the update came out.