If the mail is not coming from the same ip address where the mx record for the domain points it can still be flagged.
Also once it has been flagged as spam the first time some spam blockers may just keep flagging it unless you remove it from the black list. It all depends on the specific spam blocking going on. Its also possible your domain is on some spam black list and you may need to pursue finding out why/how it got on there and how to get it off the list.
Hope it helps,
Joe