Is there a different between triggering a process from a job or from crm application

I am using Crm process to change customEntity field -  according to phonecall set state, the phonecall state can be changed from user or from a job.

When I change the phonecall state - literally clicking the button, my customEntity field changes as expected. but when I run my job (the job changes phonecall state) my customEntity field stays the same.

BTW - the states that are being changed are from open to complete (phonecall entity).

 - before I turned to process I found out that when passing from open to complete job retunes state =1 and status 2 or 999 (will not return -1) on the other     side using the application (for the same thing) returns state = 1 and status -1. 

What can I do next to make my process fires according to my job ? Is there a way to test it ? 

Thanks