You are using the latest version correct? I can go grab a cable and double check that it is supposed to be on PC Mode I could be wrong on that. Have you tried other modes to see if it finds the phone?
Man I plugged my Maxx in when I received it replacing my OG Razr and it rooted right away and rebooted and I was done. I am not sure what is causing your issue, and you are sure you are using the latest one? The 1.40 and has the #2 option for Droid Root for 2.3.6 <motofail>?