This article on the wiki seems to identify your issue:
From the article:
Upgrading from 2.11 and have unsigned modules?
You may have come here because you’ve seen this security warning pop up, and you have a pile of unsigned modules. Don’t panic! You just haven’t completed the last part of the upgrade from 2.11 to 12. You need to log in to your FreePBX server via ssh, or via the console, and run the following three commands:
amportal a ma refreshsignatures
amportal a reload
That will ensure that all the files have the correct permissions, re-download any modules that you have on your machine that don’t have signatures. and finally click the ‘Reload Now’ button for you. After that, all the warnings and errors should be gone!