I know this is an old post, but this has just happened to me after a bank change and hopefully it can help someone else! 

Once in Settings > Payroll Settings, you must change your BANK ACCOUNTS setting and further down the ACCOUNTING setting to map the payroll to the correct Chart of Accounts (Bank)

I was lucky and found it after 2 payroll cycles, so I just did a journal entry for each to correct the account balance.

It would be nice if the Update Transactions would also fix the bank account or do the journal entry for us.