Hi Grant, we don't have communities set up yet, but have been told the setup of partner uses remains the same when we switch from portal.
I haven't run into this personally, but do the users exist as Contacts or just as Partner Users? For our portal we have to set up a Contact for every Partner User. Marketo picks up on our partner contacts but not the actual user record, which helps us reduce duplicates.
Also, do you have any constraints with your Marketo SFDC role that prevent it from seeing partner contacts?
Emily