Invalid KindleGen File
When using the Mac App Store version of Scrivener, attempting to compile to MOBI format results in an error box that reads "Invalid KindleGen file. The file at [path to KindleGen] does not seem to be a valid KindleGen file. Please try re-downloading and re-installing KindleGen."
We have confirmed that this is triggered by a change that Apple made to their "sandboxing" implementation in OS X as of 10.11.2. This change prevents Scrivener from launching KindleGen (or any other third-party process) if it is outside of the system "Applications" folder. Because KindleGen does not have a formal installer, many users are simply storing it in their "Downloads" or "Documents" folder rather than properly moving it into "Applications." Prior to 10.11.2, this did not cause any problems, but Apple has now made this a requirement to increase system security.
Move the entire KindleGen folder to inside of the "/Applications" folder. Please note that you should use the system level Applications folder located at the root of your hard drive, and not the user-level Applications folder that is located inside of your home folder. Once the KindleGen file is correctly situation in the system-level "Applications" folder, re-assign its location in Scrivener's compile dialog.