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Hi Jason,
Support for Account custom objects was introduced in Jan this year. So you should be able to use these fields in Marketo.
Can you confirm that the SFDC user used by Marketo for integration can indeed see this custom object?
May be Marketo does not have access to read this custom object in SFDC. I think most likely this might be an isse.
If that is fine, I think this will need some investigation. Marketo support would be able to help.
Hope this helps
Rajesh