If you upgrade from Compressor 1.x to Compressor 2, the old presets from Compressor 1.x may still be available in Compressor 2 within the Custom folder in the Presets window. However, these settings do not work with Compressor 2.
Even though you can select and apply these older "inherited" settings to a job in the Compressor 2 Batch window, they will produce undesirable results. You should avoid using these settings and remove them instead. To remove them:
The next time you open Compressor 2, only the new Apple optimized settings will appear in the Preset window (these are stored in a new folder at the above location). Any custom settings you create in Compressor will also be stored in this folder.
Compressor 2 settings
This document will be updated as more information becomes available.