I was wrong.. The error kept happening and I was thinking >1 second is quite a long time for authenticating to wireless. When I did pcap on both ends I could see that the larger packets were being fragmentet on the NPS and probably dropped somewhere along the way back to the AP, not sure if it was Azure firewall or VMX but they never return to the AP. I'm guessing some requests just had a smaller EAP flow. So what I saw before wasn't a timing issue, just that the AP never got the response so it kept retrying, generating the discard errors in the NPS. I created 2 new NPS policys for test and set the "Framted-MTU" to 1200 and all requests since has been granted. @alemabrahao Was right, I just didn't see the issue when only capturing the traffic on the AP.
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