Turn out my app is not actually spending 65% of it’s time in the mach_msg_trap function. It was a configuration error in Instruments on my part.
The Sampler tool defaults to All Sample Counts, this will measure all threads regardless of their state.
Instead switch to Running Sample Times that will reflect the current actual workload.
Screenshot of Instruments http://developer.apple.com/library/mac/qa/qa2009/images/qa1619_running_sample_times.png