Group migration when upgrading to Confluence 3.5

We are able to get Confluence 3.5 installed without issue. We are also able to run the script that moves the users from the older version to the new configuration without issue, but the groups are not migrated once we try to run the script that will move them. This can be problematic since we have a lot of local confluence groups. At this point we have been unable to locate any help on this. Is there any assistance that you can provide on this since we are unable to move to newer versions until this gets resolved.

Also all users are Active Directory users if that helps.

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