When you install an update to Glyphs (either through an automatic-check prompt or by manually checking for updates) and the app is automatically launched, checking for updates will find the newly installed – and thus current – version and ask you if you want to install it.
For example, I just updated from 3340 to 3342, and when 3342 was opened immediately after installing, I checked for updates and was told a newer version (3.3.1, no build number) was available.
If you quit and relaunch the app and then check for updates, it correctly tells you that you’re all up to date.
I’m guessing the current version number cached wherever it’s cached doesn’t get saved correctly when the app quits/launches in connection with an update, but is correctly saved on manual quit/launch.