Hi Doug,
So there is your problem. The counter must be running for the timer-channels to be enabled.
When Motorola first introduced the "Input Capture" function (30 years ago), they made it clear that it meant to capture "the time that an edge occured", and not just the edge itself. I don't think the documentation makes that clear anymore.
If you don't care about the time, you can save power by setting the counter to its slowest rate. But since your two input pins are spread across two different TPM modules, you will need to enable both counters.