My initial thought, (which was later confirmed by your last post about it activating your brakes albeit with the super limited information you have given thus far) is that the mapping in the phaserunner is wrong, did you load any settings in the phaserunner suite? I know they have changed throughout the iterations from reading about it, I have a frankenrunner which completely changed the mappings, and its super easy to load a default settings config that totally breaks it, I would recommend reading into the input mappings on the phaserunner.
Also, it would help leaps and bounds if you maybe included a wiring diagram when asking for help, otherwise there are nothing but questions you will get in response to your question, which obviously can be annoying, but necessary in order to help at all. If you include the basic info of this, you might have gotten more responses to your question, just a tip for next time
And finally, the manual for the phaserunner explains this exact scenario and how to fix it, I might focus my attention there and give it a little once over, you might be surprised at the wealth of stuff I bet you didn't know!