Just to be sure that everything was done according to Marketo I am adding this doc: SFDC Sync: Custom Object Sync - Marketo Docs - Product Documentation
Update us if it is still not working.
In order to help you we need a bit more detail. Which object are you attempting to create the custom field on? A standard object such as lead, contact etc, or a custom object?)
Also - you say that the SFDC-Marketo sync is working fine. What this means is that it is likely a permissions issue. We can give more advice on where to look once the question above is answered.
Chances are, if you are creating this on a standard object, you need to check field-level security in Salesforce to ensure that the field is readable by the marketo sync user.