Astronics PXIe-2461 period measurement problem

Hello everyone,

I use the Astronics PXIe-2461 Universal counter timer to measure phase shift of phase modulated signal (PM) that means one of two pulse change period in time periodaclly with out changing the pulse width and that make it hard for the PXIe-2461 it give two periods simultaneously, I thought that was related to trigger hysterisis's level and gate time settings i tried a lots of settings configurations but it didn't work.
Just for informations the PXIe-2461 give precise measure with a non frequency or phase modulated sinusoïdal or periodic signal.
Your ideas and suggestion are welcome, thank you

Here is the Pxie-2461 datasheet:

https://www.astronics.com/docs/default-source/Documents-ats/current-datasheets/universal-counter-timers/astronics_2461_datasheet-(1).pdf?sfvrsn=2

I put also the user manual in Attactched file.