Having a  similar issue. We make AJEs to correct A/R A/P on the accrual side such as writing off bad balances, adjusting balances, reclassing balances etc. and our accrual TB, P&L, & BS all come out right. When we go to run the cash basis excluding accrual AJEs and transactions the AJEs still pop up. So QuickBooks is not working correctly based on accounting standards, they're just not providing a work around. My answer is to run your accrual P&L and BS then do the trusted old fashioned Accrual to Cash conversion on your own for tax purposes. This will get you the most accurate Cash Basis Profit & Loss. QuickBooks should give you the option to run cash basis journal entries and accrual basis journal entries.