That's very interesting. Have you changed anything around that time that you noticed it behaving differently? Did you update something? E.g. WordPress, PHP, plugins, theme...
Did you enable logging to get more info from those failed transactions? WP Admin > s2Member > Log Files
Have you done troubleshooting? Plugin or theme conflicts, for example.
Are those subscriptions or buy-nows that the customers bought and are about to expire? Are those reminders for end-of-term or next-payment-time? Meaning, did they get an EOT time set, or it's just reminding them of the next payment in an active subscription?
In one of those customers with the problem, could you check the subscr ID in their WP profile and in your PayPal account and see if they match? PayPal has been changing the subscr ID format and maybe this is related to the behavior you're getting.
Any other detail you can think of?
I look forward to your update.