I upgraded to v9 as soon as it was available with no issue. DO started and converted my old v8 settings and life was good. However, every time I start DO9 now, I get a popup telling me my configuration is being converted. How do I prevent this from happening all the time?
This sounds like some artifact because of extra (non standard) items in the original Opus 8 registry keys. Perhaps put there by a plug-in or similar.
All the Opus configuration details are now in XML files and the old Registry keys are no longer used. The multiple conversion can be triggered by having extra (read non-standard) registry keys under the Opus main key.
Opus uses the presence of these keys to tell it that it need to convert the config. Essentially, under this Registry path
HKEY_CURRENT_USER\Software\GPSoftware\Directory Opus\Config\User
There should only be official keys for Leo's plug-ins. This is for \User\Viewers. So, use Regedit and have a look at this area. Please make a note of what keys you find there for future reference. (Maybe export the whole of the \User key section first?) Then delete any extra keys you find under \User except \User\Viewers...
Probably you can delete the \user\viewers keys as well since most plug-ins will work OK with the defaults and it's a good idea to reset these for the new version anyway.
Please submit a formal support request if you still have problems.
Also make sure you're using the latest version (9.0.0.7) as there were some changes made in previous versions to address this issue.