Hi Wang,
1. I use this example to calculate the frequency of the pulse ...
The counter used by Etimer module has 16 bit only, so you can't increase the range of this counter, but the clock source of both modules (PWM and Etimer) used in examples that are you talking, is 80Mhz with the possibility to use a Prescaler (divider) up to 128. So if we use 80Mhz clock source and 128 prescaler and because the Etimer and PWM module has 16 bit, then the lowest frequency that can be used is (80Mhz / 128 / 65535) approx. 9.53Hz.


If you modify the Prescaler for Etimer module (because PWM module should do that automatically if you set, let say 100Hz frequency) you should be able to measure 100hz and your duty cycle with the example. But, it is not recommended to design a project to use any hardware, mostly "at the edge" of any parameter.
The solution to your problem is to modify the clock source of the Etimer module (and of the PWM module if you needed). To do that please take a look here Clock Configuration of MPC5744P using MBD .
Other solution, if you do not want to modify clock source for this module, is to use overflow interrupt for Etimer, and at each overflow interrupt you should add 65535 to a variable until you detect a rising/falling edge and add to that variable the counts from lastest overflow interrupt, the reset your counter variable. Then if you know the Etimer counter frequency you can calculate the pulse time. But keep in mind, if you do that you should use another method to generate your pulse (not PWM due to clock source settings).
2. I observed that this example calculates the frequency every three pulses ...
I'm not sure why do you say that, but if you came to this conclusion due to this setting, then you must know that this filter is used to not count some electrical noise, it's a filter parameter that "say" to the Etimer to not count any signal that is not constant for at least 3 clock cycle after the transition. And because the next parameter "Sample Period" is equal to "0", the filter is disabled. So the period of input filtering is set by "Sample period" and how many periods, the signal, should be constant is set by the "Sample counts". For more info please see MPC5744 reference manual, Etimer module chapter, " Channel n Input Filter Register".

Best regards,
Adrian.