Loaded Commerce Community

We have set up all the vendors and added (managed) each vendors shipping methods which are all the same so we could see how multi vendor shipping works. We did also enter a vendor in each product.

Before when we were not using multi vendor the table rate (configured to only charge a fee if order is not $99 or more) and the fedex shipping modules worked pretty good but sometimes on certain products we would get screwed on expedited shipping. We were/are only using part of the fedex shipping module as I commented out everything except 2nd day, standard overnight and priority. I did the same to /includes/modules/vendors_shipping/fedex1.php and that works as well.

The problem is the table rate that I have set up for each vendor which I did the same way on each vendors table rate module. 98.99:6.50,099:0.00 should charge 6.50 for every order below $98.99 and be 0.00 for $99 or over. This is how I set it up when just using regular table rate and it worked great. Now with setting up each vendor, their shipping modules and entering a vendor in each product I can't get it to Free or 0.00 if the order is over $99. It charges the $6.50 no matter what the total is.
Any ideas as to why?