The default account system set in Membership dues batch is not honored and the Batch Revenue ends up in System Generated Account System instead. If you have a "default account system" configured (Administration/ General Ledger Setup/Assign default account systems task in top left) then it is possible that it will appear that the batch default works correctly, but it does not. If the user has no "default account system", even if the batch template is defaulted to an account system, the batch revenue ends up posting as "System Generated Account System".
We are currently evaluating this issue for a fix in a future service pack.
Steps to Duplicate
In Membership Dues Batch set the default account system to desired Account
Go to Payment and Notice on GL Distributions tab that the Account system: System Generated Account System