Try opening the "Software Updater" app instead of "Software & Updates". Does a list of updates appear? (After a fresh install of Freya, you should see a bunch of updates.) If you click "Details of Updates", do you see anything other than "Elementary Base"? If so, those are most likely from trusty-updates or trusty-security.
If you answered "yes" to both of those questions, then your updates are working properly, and the Software & Updates app has a UI bug. It's frustrating for sure, but I believe this app is slated to be removed in the next version of Elementary and replaced with Elementary's own software center.
The good news is that unless you plan to add third-party PPAs, you can generally ignore the "Software & Updates" app. The fact that Ubuntu has a Software Center and two different "Software Update" apps drives me bananas, personally! :)
I'm experiencing this issue, and Software Updater is telling me I have no updates. As far as I can tell, third-party PPAs that I added are misbehaving, and Software & Updates is doing a poor job of explaining exactly what has happened. Here's how I fixed it:
- Open the "Software and Updates" application.
- Go to the "Other Software" tab.
- Look for third-party PPAs, and disable them. The third-party ones will have a URL (not a name such as "Recommended updates"), and that URL won't start with
- The checkboxes in the updates tab still won't check. This is totally fine.
- Run the "Software Updater" application. You should now be able to get updates. If you click "Details of Updates", you can see the actual packages that will be updated.
Optionally, after things are fixed, go back and re-enable PPAs one by one and see if anything breaks.
Possibly related: this bug in Launchpad.
Edit: Here's an Elementary ticket for this bug. Looks like the bug will be fixed in 0.4.