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This sounds like it may be a permissions issue in SFDC.
To test this, log into SFDC as the Marketo sync user and see if you can navigate to the campaigns that are not showing up in Marketo. Verify that they are also active at this time.
Thanks Will. There are no permission issues and as I said, all the campaigns are active.
Go ahead and open a support case. If the campaign is active and is visible to the Marketo Sync User, it should be selectable in Marketo.