First, think I'd backup what's there ... full site backup.
Then manually remove the contents of the following moodledata directories:
cache localcache muc and sessions.
Moodle should repopulate.
'... every new update ...' are we talking like the weekly releases? Wow! Hope you are doing those via git and not the old fashion way.
Check the version.php file at code root. What's the build date?
If you are using git, check the branch being tacked with:
git branch -a
and look for the line at the top with * ... what does that show?
'spirit of sharing', Ken