I've seen a couple of issues raised where command line parameters' actions were inverted. I wonder if this is one of them. Try un-checking the box. If that fixes it then you should raise an issue in the github project.
Using ABSPrusa Mendel Zaphod with Pronterface and slic3r 1.3.0. Printing well with 3mm PLA and ABS through 2 x J Head Mk IV b and Wade Geared Exruders. Controlled using RAMPS1.4 board running Marlin_v1.1.9