I will confirm this happens to me sometimes also on 16.04 on several different 
machines.
I have debugged as well and will also confirm it has to do with the file dates 
and how long an update takes, so it is not easily reproducible.  But the logic 
flow shows how it can happen.
I have patched the updates_available script as shown above to add the third 
check, thanks so much.
Before that I was thinking about having the update be done in a sub-script and 
at the end of that touch the cache file, so the sub-script would still run in 
the background but the cache file would get a more recent mod time.

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https://bugs.launchpad.net/bugs/1604750

Title:
  Byobu not clearing update numbers after updates

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