New Retroactive F&A process for Grants (GM_RTRO_FA) processing

We are in the process of upgrading from 9.2.4 to 9.2.18 and have spent a bit of time testing the new retro f&a process.  Our findings are showing that this process is unusable as it currently is.  I am wondering if we have missed a configuration setting or set up somewhere along the line.  What we are seeing;

1.  Processing against the new effective dated logic for Project Department - The process recognizes that there is a new department to create the offsetting F&A transactions for but it doesn't take into consideration the effective date.  It does it for all transactions.