I am still having this issue.  Just built two machines with a fresh
Ubuntu install for dual-booting with windows.  After an upgrade I
attempted to install both Chrome and Brackets.  The software manager
rarely appears to prompt for system password when attempting to install
3rd party packages, it just sits not doing much.

On occasion after reboot I am able to install a single 3rd party
package, which I get prompted for a password for, but most of the time I
receive no prompt and the package install hangs.

As OP notes, there is a shift in formating on the page when clicking
'install' for the first time.  On occasion I am then greeted with a
password input pop-up (although this has only occured with a Chrome
install, and even then only after multiple reboots, I have been unable
to install other 3rd party apps.)

Clicking on 'install' for a second time places a 'Waiting to install'
icon in the sidebar, right clicking on this icon give an empty menu, a
seperator, and then a 'Lock to launcher' menu item that does not appear
to do anything when clicked.

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https://bugs.launchpad.net/bugs/1573408

Title:
  GNOME Software does not install third-party .deb packages

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