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I'm receiving a message about multiple input/output paths when using dual unit mode with Pro Tools 9

Pro Tools 9 requires each input/output path to have a unique name however when using dual unit mode the input/output names set by the driver are duplicated. In order to resolve this you need to edit the name of all input/output paths for the set of input/outputs for the second unit. You can simply put a 2 after all inputs/outputs (see below).