It appeard that all my entries in HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Run were gone (except for Opera Browser Assistant). I have a very strong suspicion, that the auto-updater not appended/update the Run registry entry, but wiped it completely.
Same happened to me, when i reinstalled Opera!
I'm not sure, if it was done by uninstall or by reinstall.
But afterwards the whole key ("HKEY_LOCAL_MACHINE\SOFTWARE\WOW6432Node\Microsoft\Windows\CurrentVersion\Run") with some other needed(!) startups was gone!
What luck i backuped it just before, to document the Opera-entry.