Costing of Inventory Transactions

We have raised the issue that the cost accounting creation process uses the transaction date time stamp to pick the effective dated cost.  We are new to 9.1.  Either 8.4 used the transaction date for this process or we had it modded for that, but 9.1 is definitely uses the date time stamp for costing purposes.  This is an issue for us.  We have a 12/31 fiscal year and we sometimes count inventory on 12/31 or 1/1 or 1/2.  We are making inventory adjustments after the year end relative to the prior year.  We back date the transaction date to