Operaprefs.ini only exists in Presto (12-) versions of Opera, not in the Chromium (15+) based versions.
Opera version 15 and higher will not replace earlier versions.
If you want to use later Chromium versions only, you should install the later version and import your bookmarks into the new version, and then uninstall the earlier Presto version manually.

Opps! I see I was looking at an older folder I still have on my Windows machine. I am using Opera 24, but saved the folders for Opera 12.

This looks like the equivalent in Opera 24. I would try deleting that.

C:\Users\YourUserName\AppData\Roaming\Opera Software\Opera Stable\preferences