Take a look at the Global Time Base (GTB) option (if the 03 has it, I'm more familiar with the 27).
Without using GTB there is no guarantee that the TPM0 and TPM1 are in any way synchronized.
Without knowing more about your set up I don't know if that is important.
It may also be possible to do something with the event triggers.
I use this format to play Nokia Ring Tones. Via using DMA the various clock latencies and synchronizations are taken care of at the hardware level:
* Alarm sound sequence are done by pointing DMA at first sound sequence in tone table.
* When the end of that table is reached a DMA IRQ happens that loads the PIT silence timer.
* When the PIT silence timer expires it loads next DMA tone sequence.
*
* DMA -> PIT -> DMA -> PIT sequence repeates until the last state is
* reached in the state-machine that starts it all over again.
Doing something alone that line will probably lead to less phase discontinuity.