An IPsec tunnel is agnostic of the protocol inside. As long as it's IP. Use tcpdump to trace the packets:
source incoming interfacesource tunnel interfacedestination tunnel interfacedestination outgoing interfaceThey get lost or are blocked SOMWHERE. Depending on that somewhere a firewall rule, NAT rule, ... might be at work here.
I remember a problem with udp fragments and radius EAP over the tunnel. Really strange problem