The tray icon on my system is showing the availability of new updates, however they don't show up in the updates tab within Discover. Manually making Discover check for new updates won't help. The updates are available though, since manually starting apt-get upgrade via console is fetching them. Similarly, when I do sudo apt-get update and updates are available, the tray icon will show the availability of updates, but no updates show up in Discover. This problem usually seems to fix itself after some time, when Discover finally discovers the missing updates by itself (as I said, manually making it check for updates usually does not work). This is on Kubuntu 16.10 64bit.
This problem is known and was fixed in 5.8. I advise updating. There's a backports repository available for kubuntu 16.10, as far as I know.