Windows executables come in two flavours. GUI executables and CLI executables. Windows will always pop up a new CMD windows when a CLI executable is invoked by a GUI executable. This behaviour is especially annoying for background jobs.
The Quick & Dirty Solution:
Running command-line tools without a CMD window on Windows is tricky. The quick and dirty solution is to call CMD minimized using the following trick:
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cmd /c START /MIN cmd /c filebot -script fn:amc ...

Instructions for µTorrent:
We can use pythonw to call python scripts in the background and then call filebot from there. Calling filebot from python instead of µTorrent also makes it easier to pass in custom options or perform custom operations before or after the amc script is called.
- Install Python and restart your computer. Call python --version to make sure that python is installed correctly and in the $PATH. Please use Python 3 or higher.
- Fetch (right-click, Save As...) the utorrent-postprocess.pyw python script and modify (open with Notepad++ and edit) it to your needs:
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# configuration output = 'X:/Media'
- Set Run Program to your script and pass in all the µTorrent variables via command-line arguments:
Note: pyw files are executed with pythonw.exe which is a GUI executable and so it won't pop up a CMD window.
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"C:\path\to\utorrent-postprocess.pyw" "%L" "%S" "%N" "%K" "%F" "%D"
Instructions for qBittorrent:
Same as the above, except that we call utorrent-postprocess.pyw with the appropriate qBittorrent variables:
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"C:\path\to\utorrent-postprocess.pyw" "%L" "" "%N" "multi" "" "%F"