Automatic WT is not deducted from the /560

Dear Experts,

Am working positive Time management, accordingly if an
employee came 1 hour late to work a wage type generates automatically with the
amount, this wage type has to subtracted from the basic salary first and then
calculate the taxes(till this point it is working correctly).

The problem is this amount of the automatic WT is not
deducted from the /560

Note: when I enter the same wage type manually through
infotype 15 the amount is correct in the payslip too and it deduct it from
/560.

Thanks,