This issue has been fixed in the Braintree update as far a i know. I believe the root cause was a bug in the migration code which would migrate the internal path from an earlier version of SONAR. In fact it would migrate from SONAR X2 if present rather than SONAR X3. In Braintree I now restore the proper internal path after the migration process.
However users who already migrated earlier might still have the bad path in there. Your work around is good. Alternatively users can force migration again after installing Braintree to fix it up. This may or may not be a desirable solution however since any post migration customized settings would get lost.
To force migration again go to HKEY_CURRENT_USER\Software\Cakewalk Music Software\SONAR\Platinum
Then change the value of Migrated Existing Preferences to 0 and restart SONAR.
If you don't feel comfortable editing the registry call tech support and they can help you. Users who didn't migrate shouldn't have had this issue.