The newest version of HandBrake, 0.10.0, breaks the ability of HandBrakeBatch to read your custom presets. There have been some changes in the format of the file containing the presets, and HandBrakeBatch is not yet able to parse the new format. The application will still work, but will fall back to the default presets.
If custom presets are important for you, and you still want to use HandBrakeBatch, do not update HandBrake. If you have already updated, you are out of luck for the time being. I plan to spend some time looking into this during the Christmas break, so possibly I will release a new version of HBB before the New Year (no guarantees).
In the meanwhile, even if it is not so convenient, you can still use HandBrake to manage your batch conversions.