Hi all,
I've definitely solved the issue! ...and I'll try to explain what I've done.
The problem is not related to TU1/TU2 timers but is related to the content of their IRS routines. I attach 2 KDS projects (InputCapture-Issue and InputCaptue-Ok) for better understanding of the problem.
On the InputCapture-Issue project I've implemented TU2_OnCounterRestart ISR with 5 GPIO outputs setts. In this case, these GPIOs are defined using PE as a GPIO_LDD group-of-bit-fields component (see next image)

In contrast, on the InputCapture-Ok project the 5 GPIOs are defined as single BitIO_LDD components as shown:

For the InputCapture-Ok project GPIO implementation I see no missing pulses on CapX_OnCapture ISR routines. Obviously, I can not say the same in the case of the InputCapure-Issue project as I can detect missing pulses.
Please, could anybody verify this behavior?
regards,
gaston