Hello Doug,
Yes, there is a coherency mechanism for updating the 16-bit registers within the TPM module, including TPMxMOD. The channel registers are also affected, and unfortunately there are signiffican coherency mechanism differences between V1, V2 and V3 modules. The following post addresses update of channel registers for V3 modules, and may be of general interest.
https://community.freescale.com/message/62954#62954
To achieve immediate update of the TPMxMOD setting, I suggest this should be done with the TPMxSC_CLKS setting at 00 (clock disabled). Update should then occur when the second byte is written, and will be independent of the prescale setting. Otherwise, the update would be delayed until the next TPM clock edge, from the prescaler. Within this period, it is possible for other TPM register writes to clear the coherency mechanism, so the value never gets updated.
Another possibility is to test and wait for the updated value before any other TPM register writes.
Regards,
Mac