Yes I called up KLM customer service. Apparently it's their policy now to charge each air ticket separately to the credit card even if it's all within the same booking/ transaction. So checking out is fine, shows the total bill but not the actual billing. Btw they charge $20 for credit card payment online too.
I see, thanks for the info. Scoot also charges a $20 credit card processing fee. Jetstar I think is $9 but you can pay via vbox.com.sg to avoid that charge (though I have never done that before).