I just ran our land dates through the disney site for fun and it came up $200 cheaper!
Did you then add in the resort taxes (c. 12.5%, but can vary slightly by resort location)? How about
trip insurance--is it included in both? Those $$$ can add up, and may account for the difference between what you came up with online, and what the TA quoted you.
Also, double check that both quotes include exactly the same ticket types in terms of the options (base, PH, pluses, non-exp.?), and the same room category (standard/garden view, preferred, concierge, etc.). You should make certain you are not comparing 'apples to oranges'.
If you double check all of the above, and still come up with a significant difference in pricing, then ask your TA why that is. Most TA's do not charge the customer a fee... but some do. If the $$$ don't add up, and the TA can not provide a reasonable explanation, THEN I'd drop the TA and book on my own. But I'd give them a chance to explain, first.
