First of all, if booked as a "room only" that is cancelled and rebooked in a different system by Disney (when the TA calls Disney) as a "ticketless package." There is such a thing now, but it's not on a TA's screen and must be called in. Not all TA's are aware of it, it's fairly new in the last year or so. If the TA does much booking with Disney they SHOULD be aware of it.
Some TA's have a block of rooms at special rates that can't be booked as packages, so can't add dining or tickets to those.
What you want is a "ticketless package". Either tell the TA they have to call this in for you, or cancel the room and find a new TA, or book the entire package yourself. A good TA is worth the time, but some just don't know Disney!