Installing a new extension also leads to asking to run the upgrades
When you install a new extension (for example CiviRules). It will ask after installation to run the upgrades. As soon as you have run the upgrades and disable and uninstall the extension it will never ask for it again.
I have seens this behaviour since a couple of months and I do think it needs to be fixed by setting the schema_version in civicrm_extension after an extension is installed.