I have had similar problems with my corporate travel agency. After several late checks in and getting stuck with smoking rooms, I found out that it seems the agency can only enter the non/smoking "request".

Thus I always now call Marriott after placing my reservation through my corporate travel agent and have Marriott "confirm" my preference. Very inefficient and annoying but it beats the alternative.

[This message has been edited by hershmeister (edited Dec 24, 2003).]