@skasoff Thank you for that information.
It sounds like there may have been a manual payment previously received for those customers and the "Process Payment" box may have been left unchecked.
QuickBooks is designed to remember settings placed. Sometimes customer payments need to be recorded against an invoice but not processed, when this happens the "Process Payment" box is left clear to prevent electronic money movement.
Subsequent invoices will not be enabled to take credit card/ACH payments unless that box is checked. You did the right thing by re-sending the invoices with credit card processing enabled. You should not run into this problem again unless settings are changed.
Let me know if this helps.