What custom field did you create on the SFDC side? How does it apply to what you are trying to do? I've noticed on Opportunities that if you can add the constraint, but no values appear in the drop down, you can still add the values you are looking for manually and Mkto will be able to filter based on it. I would recommend finding one record on the SFDC side you know should satisfy your criteria, then add all of it's information on the Mkto side through filters and see if the record shows up. Just a way of double checking that the filters are working as they should.
This could be a weird sync issue though, in which case I would recommend contacting Mkto Support, but I will continue try to help if you want someone to bounce ideas off of.