Here are two things to try:
- Try disabling the auto-update setting: 1) Disconnect from the internet, 2) disable the setting, then 3) quit Joplin with file > quit.
- "Enable auto-updates" is not to be confused with "Automatically check for updates".
- "Enable auto-updates" is disabled by default, so might not be enabled.
- Switch to a pre-release version of Joplin (e.g. v3.5.6). Be aware of this comment about compatibility with older versions before upgrading.