I know nothing for a fact, but I think that certain rooms are allotted for
free dining at a time, and there may be rooms available at a certain resort, but not for free dining.
Easiest way to check is to see if there is availability for room only on the Disney site.
Now if you are asking if a
Travel Agent has rooms for free dining at a particular resort I suppose it can't hurt to ask.. I would think they got their "sections" of rooms available for free dining and might still have availability..
Calling disney up to and around the 45 day mark for your dates might get you the promotion, as people have to pay in full for their vacations by 45 days and might decide to cancel. But will the window be open to book at 45 days?
Have you considered any other resorts? I probably would take free dining wherever I could get it myself. Then you could keep checking to see if anyone cancels for your dates.
Good luck and hopefully someone who understands Travel Agents better will have good advice!