When I've had problems with Fabric.com they correct it right away. Their cuts are at least 1 inch over and several times have been more.
I have placed 5 orders recently with Connecting Threads. I have found their fabric to be of very high quality, not thin at all and surprisingly thicker than many of the big name fabrics. They have not shorted me either and, as a plus, they are very close to on grain or are on grain. With the Fabric.com fabric, that extra bit is often eaten up or nearly so by the fact that they're not always straight cuts. At Connecting Threads I have ordered fat quarters and very often get an extra piece with the fat quarters. I'm not sure why this is. I have measured to see if the fat quarter is short, but that has not been the case. I do like the selection at Fabric.com better in that they often have some of the latest lines but often not very much of it but with their coupons and free shipping over $35, usually I can get a very good deal. Sometimes I can get the same name fabric cheaper at other sites such as Old Country Stores or Fabric Depot.
I can't imagine that you were given a hard time at Connecting Threads as they have been so very nice whenever I've called with a question. As I've had no problems with my orders I can't say how they have been when a problem has arisen, however. I would call them again and tell someone else what has happened as it is possible that you and the first person have somehow misunderstood each other. I think with all the positive experiences here with that company that you should try that approach. I know I would do so and state that you think that there must have been some misunderstanding. Good luck.