I would start analyses of this problem with the simplest packet which expected to be replied by MSTCP – ICMP ping. It has simple structure, so it must be easy to verify that the packet which you indicate from the name of the WAN interface after decapsulation is OK.
I have one idea regarding problems with WAN you have, what MAC addresses do you have in the Ethernet header? If when operation over LAN it does not matter much, then over WAN you must use pair of MAC’s associated with particular WAN connection. In your case you must use MAC’s from the original (UDP?) packet received over WAN, but not the MAC’s that packet had before encapsulation or any other MAC’s. Otherwise NDISWAN fails to associate packet with the particular WAN connection and silently drops it.
May be this is not your case, but this is one of the common problems with WAN. If it does not help then please provide more details and I hope we will be able to figure out the exact reason.