Paycheck is not distributed properly between accounts

I have been having trouble with my monthly paychecks not being logged properly in Quicken. I recently even went so far as to delete my paycheck setup and recreate it from scratch. It only works differently now - still not correctly.

My paycheck is deposited to three different accounts at three different companies (although Bank of America and Merrill Lynch are two of those). The Merrill Lynch account is primary, receiving the remainder after set amounts are deposited in the other two accounts. After receiving my paystub, I entered my monthly paycheck information in them Bills & Income dialog, which shows all three accounts entered properly, before I downloaded the information from my banks. Now, the two set-amount accounts deposit OK and clicking the Split Transaction window icon in those records does open the Edit Current Paycheck dialog. However, the primary account arrives after download with category= "[Flex Spending]" (another account, which receives the Flex Spending Account deduction from my paycheck) AND a debit is added with category "--paycheck--" that transfers the deposit to the outside bank from my Merrill Lynch account, to which the amount is NOT DEPOSITED, to that external bank (not Bank of America).

To correct this, I have to edit the debit from my Merrill Lynch account (having the amount deposited in the external account) to be a deposit of the correct amount that is erroneously set to the "[Flex Spending]" category and also copy the Memo field to the "--Paycheck--" line I edited, then delete the "[Flex Spending]" line.