I figured out that the problem was from when the timer period was read during the trace initialize the value was 0, and that was causing the problem from the first post. The timer period does get set but not until the scheduler is started.
For now I just hard coded the timer period to the value used and that it good enough for my testing now.
#define TRC_HWTC_PERIOD (333334) // (TRC_CA9_MPCORE_PRIVCTR_PERIOD_REG + 1)