Thanks for the feedback. That shed some light on the problem.
Ok, I've looked at some of the source that came with the eTPU set that we downloaded. It appears that all of the code uses the GreaterEqual setting. From David's comment, am I correct in assuming that the code set would need to be recompiled using the EqualOnly setting? Is there a version from Freescale/NXP that can be downloaded with the EqualOnly setting? Or do we need to get the ByteCraft compiler and recompile ourselves?
BTW, I tried changing my timebase from TCR1 to TCR2 but the input capture exhibited the same response. That's what led me to examine the code set and where I saw the GreaterEqual settings.