I had a client pay for 2 domain renewals in one invoice this morning.
The .com domain to be renewed, renewed with our registrar, ENOM right away. The .ca domain to be renewed has not yet renewed as of yet and it's been 1.5 hours now.
The .com domain's expiry date also did not update within WHMCS (just the Next Due Date updated to 2017).
WHMCS Version: 6.3.0 (updated on April 3)
Auto Renew on Payment is Enabled
I didn't notice this problem before WHMCS was updated April 3rd.