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Due to a bug in the kernel driver for the Apple Magic Trackpad, two finger right click doesn't work by default. However, you can fix the issue by running the following:

xinput set-prop $DEVICE_ID "Synaptics Click Action" 1 3 2

...where $DEVICE_ID is the device id given for the device in the output of xinput --list.

Due to the nature of the device (Bluetooth) it's not always connected. Can I run this fix script every time that xinput detects the device as connected?

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Did you find the answer to that? –  Mashimom Feb 28 '14 at 21:43

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