I was having the same problem until I realized that I needed to download the Avivo converter file separately of the Catalyst Control Center. If you go to the ATi driver download page and search for you operating system and card you should get the results page. Located toward the bottom of that page should be the Avivo Package. After I installed this I was able to select 'GPU Acceleration' for encoding.
*Please note that this is not available for all types of videos!
This works for Mpeg2 and .H264 videos but I don't think it works on anything else (such as streaming types like .wmv).