Churn Report issue

[Deepika]

Our client runs a SaaS portal and uses Freshbooks to do monthly billing of subscribers. We setup a subscriber initially and bill him setup fees, but recurring monthly billing starts in a few months (2 to 3 months)  time after we have done setting up of users and training them. Due to discontinuity between first billing (setup) and subsequent billing, Freshbook thinks we lost the customer and our churn report shows lost clients that are not actually lost. 
How to fix this ? I am looking for suggestions. We would like to do as much work as possible on Freshbooks platform, and not introduce another platform to export data and create reports.