I have this problem from time to time as well. You have to make the sequence in FCP 16×9 anamorphic. I have tried it using a Pro Rez sequence and an uncompressed sequence. The only way I have made it work is with a DV anamorphic sequence. When you drop the reference movie into Compressor It automatically knows it’s 16×9 anamorphic. I have not been able to get compressor to do this with anything but a DV sequence.