Opera fixed this a while ago. It no longer puts the troublesome entries in the Preferences file. But, if the entries are already there in the preferences file from a version of Opera that had the problem, you'll have to remove them yourself or the issue will never be fixed for you.
It cannot be said that it was fixed, Opera must come with a full-fledged fix which modifies the preferences accordingly during an update, without requiring any user intervention. Please realise that most of the users don't know what is the cause of issues on their PC because the issue affects other programs, so they have no idea how to fix it.
If this issue is not going to be fixed, it is a very good reason to uninstall Opera to prevent further issues.