I just ran into this issue, I haven't used clone or import but due to the fact that pathauto can't use "#" I am using eca to set the path.
Now i noticed i couldn't set set the url alias manually or with eca, even un-installing path-auto didn't solve the issue because sub-path auto was installed also.
I had to un-install pathauto and sub-pathauto and than i could manually or with eca set the path alias.