Hello Bob,
I presume you will be using interrupts on the TPM channel. If you need to explicitly control the output state resulting from an output compare, I suggest you don't set for toggle mode. Instead, select either set on compare, or clear on compare, from within the ISR, to correspond with the opposite of the current state. The current state would be indicated by bit-2 of the channel status and control register.
When initialising the timer channel, and prior to enabling interrupts, the initial setting should clear on compare. You could also read the current timer counter value, and set the initial channel compare value to occur a few timer cycles hence.
Regards,
Mac