Why would an incorrect amount entered in box 26 affect the refund amount? Entered $5590 instead if $55,900?

If it's from a T4 slip, the amount of pensionable earnings could be affecting the amount of CPP due - ie if you had the proper amount of CPP deducted for $55K, you would have overpaid on earnings of $5K - resulting in a CPP overpayment.