The Traffic alert and Collision Avoidance System (TCAS) was designed to prevent mid-air collisions by portraying a time-critical "resolution advisory" (RA) to the pilot. Complying with a TCAS RA is generally considered the safest course of action and takes priority over all other forms of air traffic management; however, pilot compliance with TCAS RAs is surprisingly low. One proposed solution is an 'Auto-RA' function which couples the autoflight system to TCAS such that, when the autopilot is engaged, it automatically executes any corrective RAs. This paper describes a study in an integrated flight deck/air traffic control simulator examining how pilots interact with TCAS with and without an 'Auto-RA' function. A prior study found that pilots allowed the autoflight system to fly the RA maneuver in 83% of the runs, but the situations where the pilots disconnected the Auto-RA function generally involved scenarios where pilots received confusing guidance from the RA, and conflicting instructions from air traffic control. Further, once clear of the conflict, pilots appeared to have trouble remembering which autoflight modes they had had engaged before the RA, and air traffic instructions requiring particular speed or altitude targets that were effectively erased by the Auto-RA function. Thus, this study particularly focused on particularly problematic traffic encounters, and on situations where the Auto-RA might disrupt pilots from meeting a specified air traffic restriction.