It would appear it's something to do with AppTranslocation process.
Interesting that it will go away after a period of time or moving things around.
I'm suspecting by signing up as a known-developer I may be able to bypass/resolve this situation more directly?
Updating for my own information and future searchers;
To resolve this, it appears you can fix it using the xattr command to remove the ranslocation / virtual-folder situation
xattr -dr com.apple.quarantine ./folder/of/interest