If both tuners show up in MC (they should), I can not imagine why there is a conflict. MC should be able to use both tuners. I have an HDHomerun. It works fine.
Did MC pops up a message telling you there is a conflict while you were doing scheduling? If so, did you check to see if you had some forgotten subscription already scheduled at the time slot?
Or, is it just that MC did not record the second show that you scheduled?