[KevinH]

FWIW, I updated to 10.12.3 and downloaded a fresh copy (this time of version 3.0) and tried to launch it but got the "Unidentified Developer" message. Then right clicked on it, selected Open and then hit the Open button when asked if I was sure and then cancelled out after a successful launch.

Had no trouble then dragging and dropping folders to create epubs. It all works for me but I have full XCode and Command Line Tools installed where-as many other users will not.

-- ps

It seems Sierra will prevent any zip dmg, or application from running from the "Download" folder as part of its Sierra Gatekeeper Improvement. You have to manually move the zip/dmg/etc out of the Download folder using Finder (manually - not by command line or script or any other way).

Until you do that, Gatekeeper does the equivalent of copying it to a randomized path location that is effectively a read-only/locked dmg image before running it. This breaks most installers and many programs as they can not find their resources. It will keep doing that until you manually (using the Finder) drag the zip/dmg/executable out of Downloads. There is probably an extended attribute you can delete but I am not sure about that.

Perhaps this is what is going on? People did not use the finder to move the zip our of the Downloads or tried some other programmical way to move it) and are now stuck with versions that will not work.