I have seen similar issues where some components in the path between AP and RADIUS server did not allow the large packets to come through. I have seen such issues solved by changing the vSwitch in VMware to allow jumbo-frames.
What appears to be happening is that the EAP RADIUS packets are dropped when they need to be fragmented (or are fragmented); I first saw these issues appear when certificates no longer supported MD5 signatures. In your case, it is probably the RADIUS server certificate that gets fragmented/dropped, as EAP-PEAP (MSCHAPv2) does not send large frames from client to server.
What you can try to do is reduce the MTU on your RADIUS server, to prevent the RADIUS packets being fragmented on their way to the AP.
It may be wise to do some packet captures in order to find out where the packet is lost/fragmented. If you can solve the fragmentation, that may be the better solution versus tweaking MTU on servers.