Network traffic within a VPC

I can't think of a good reason why you'd be seeing intermittent network connectivity here. I'd strongly recommend that you raise a support ticket to investigate as the support team can delve into the instances and network services that you're using in order to troubleshoot. On re:Post we have no visibility into your account, services or anything so the support team is best positioned to help.

That said: You haven't mentioned which region you're running in nor which instance types you're using. The first is just for interest; but the second might have an impact - smaller instances have less bandwidth available to them - if there is a lot of other traffic between the two instances then that might cause some issues.

+1 to what @Brettski mentioned. Additionally, to rule out OS (windows) specific issues you can spin up Linux EC2 instances in the same exact subnet and see if exhibits same ping/packet loss also? This will help you narrow down the troubleshooting scope. It sounds like both your source and destination servers are windows currently.

Secondly, refer this KB article I know this is not VPN related issue but there is 1 Windows related setting (See the section: Explicit Congestion Notification (ECN)) that is suggested to toggle. You may want to give it a try, if it does not resolve the issue you can simply toggle it back.