A couple of hours of layover during my flight to Italy gave me just enough time to fix the issue with custom presets, which appeared recently in HandBrakeBatch. The problem was due to some changes in the preset file format, introduced with HandBrake 0.10.0. I am not on my main computer, so I do not have many sample files (neither preset files, nor sample movies), but the new version loads my custom presets correctly.
The issue was related to the way preset folders are encoded in the file: it used to be a boolean and it is now an integer. I do not really understand the reason for this change, but it was relatively easy to fix once found. I have only changed the script which translates the preset file in command line options for the HandBrake CLI, so the risk of regressions is small. That said, there might be other changes in the format of the preset file which I missed, so if you have problems let me know.
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On this, Merry Christmas and Happy New Year!