Sounds like it's not catching the build events properly to see that it needs to update stuff. That's all old code, so it's quite possible changes in Factorio's events means it's missing some cases.
Playing with it myself, copy/pasting with robots works fine, but using creative mode with the instant blueprint option enabled doesn't. That uses the script_raised_revive event which isn't caught, so I'll need to add that. Are you running any mods that change how things are built, or doing this in editor mode?