Symptoms

Was not given the option to upgrade the app in the App Catalog

Trying to use sharepoint app - tells me SmartObject Out of sync ... A new version may be required.
Browsed to Site Contents, and selected the Upgrade link from About - it tells me 'Good News you already have this on your site'.
Tried to Register - it tells me A newer version of the App is available.

I have tried removing the SharePoint App and re-adding it. It gives me
 

Diagnoses

There appeared to be an issue with having the App Catalog on a root Catalog.

As well as permission and port requirements.
 

Resolution

This issue was resolved yesterday with the help of LABS

It seems like the issue was due to them having the App Catalog on a root site. Even though the necessary permissions were given, everything was setup correctly etc. The app deployment would run in to errors even though it passed green in the analysis.

This also seemed to break the app registration, and even though after updating the app, it showed that it was on the correct version. We had to remove the app and Labs manually added it again without any metadata, and this allowed us to register the app on the site.

We also had to run the cert management tool to sync the certs as the had 2 k2 environments pointing towards the same SP site. There were a few extra steps, IE Oauth Repair, etc that we had to run through, but that was due to other issues that we ran in to during the initial stages of the investigation, as well as opening port 6332.