When there are two payments, I believe one is for savings balance and one for regular balance.

I manually checked a few accounts and didn't see any transaction related to this

The interest won't be paid unless there is a transaction. This applies to both regular and savings. This doesn't mean the interest isn't be earned, it is and continues to accrue. It just isn't actually paid out until there is activity. This does mean that any compounding (earning interest on the interest) won't happen.