Process builder flow not working for automated processes

We have set up a process builder flow as follows
> Created a checkbox field 'isActive' on 'Entitlement' Object
> Created a process builder flow and updating the field 'isActive' i.e. 'isActive' is checked or unchecked based on some conditions
> When I edit the record manually to meet the criteria process builder flow is working properly
> But for automated processes which happens in the backend and meet the criteria , the 'isActive' field is not gettign unchecked.
Please help me to find out what would be the reason and why it is not woking for automated process.

Thanks,
Anupama