I am sorry, but your answer missed the point of the issue. I can rewrite the issue i have as follows: 

Bank transaction history: 

Transaction A -$2000

Transaction B -$750

Transaction C -$1500

QuickBooks log after i synchronize with bank is as follows: 

Transaction A -$2000

Transaction B +$750

Transaction C -$1500

My bank states that my balance is -$4250, my QuickBooks P&L says my balance is -$2750. That is the core issue, QuickBooks flips a negative transaction to a positive transaction. It has nothing to do with processing fee, nothing to do with journal entry or accountant consultation.