Forces due to alternating flow states on the payload fairing of launch vehicles can couple with structural responses during transonic flight. A new methodology for the assessment of this type of self-sustained oscillation is applied for an actual launch vehicle mission. Corresponding internal launch vehicle loads are compared with those for the other transonic airloads events. The limit cycle amplitude from the analysis is compared with that from application of an existing technique in the literature. It is shown that the new methodology can be significantly less conservative than the stability criterion for bounded system responses. The historical assumption that the alternating flow forces on the payload fairing couple with a single launch vehicle bending mode is investigated through transient analysis of the fully coupled system. Evidence of alternating flow separation in flight data for the Titan IV launch vehicle is presented.