Hi Michael,
As you mention, only the first interrupt happens after 1 ms because that is the time it takes the counter to go from 0x0000 to 0x4E1B, after this the next interrupts will happen every 3.27ms, this is because that is the time it takes the TPM to count from 0x4E1B to 0xFFFF and then from 0x0000 to 0x4E1B again:
1/19995000 (bus clock) = 5.001e-8
5.001e-8 * 65535 (0xFFFF) = 3.2777ms
If you want to generate an interrupt every 1 ms I would recommend you to use the Timer interrupt component instead of the free counter component.
I can upload an example that uses the Timer interrupt to generate an interrupt every 1 ms for your reference, just let me know the CodeWarrior version you are using.
Best regards!
Carlos Mendoza