Update to this!
I believe it has to do with a new Sierra gatekeeper security feature. The thing to google for here is "App Translocation". When someone tries to run an unsigned app from it's original downloaded (or unzipped) folder, OSX mounts it into a temporary read-only disk image and executes it from there. This is why it will show up in a
By manually moving it, it unsets a quarantine flag that let's it then execute normally, and it will report it's location correctly. It will also let you create folders/log files normally again. Moving with the command line does not unset this flag.
There is a lot more to it, but that should be enough to start help debugging this problem.