I was also having this issue, as many others I have found in other forums.
After a bit of testing, I found that if I try to click the link "Attempt CC Captures" right after cron runs, it would not capture the payments, it was as if WHMCS could not even see the payment method. I tried clicking the "Attempt CC Captures" about 8 hours later, and it worked.
I then switched my cron to run at 12 PM instead of 4 AM, after switching this my automatic payments started working. I have only had it running at 12 PM for 2 days, however this is the first time it has worked for all invoices with a payment method.