I’m not familier with IPSECVPN software you use, but yes, there are two possibilities:
1) IPSEC driver above WinpkFilter: in this case instead normal TCP/IP packets (all or only part of them depending on IPSEC policy) you intercept encrypted IPSEC packets. I’m not sure how your WinpkFilter software would deal with these packets (tries to tunnel or ignores).
2) IPSEC driver below WinpkFilter: in this case your UDP tunnel packets can be encrypted by IPSEC driver (depending on the policy).
I would check what packet you get in your WinpkFilter software and check what packet go out on the network media with network sniffer to discover the details.