I don't know where the issue is coming from but it seems that VPN users cant see each other. What I mean mean by that is if both use VPN they cant search the other person and leech files even if they have it or just show as offline even when there on. But if one of the two user stop using a vpn then they can connect to each other like normal and view each other folders and message.

I would like to know if this is a known issue and if so what are fixes for it or if its a new issue.

I think I've observed this too.  Depending on the VPN service used, VPN users may need to enable port forwarding and specify that port number for Fopnu.  In addition, TCP/UDP ports cannot be used by 2 or more programs simultaneously.  So if port 12345 is the VPN forwarding port, you'd have to specify that port in your P2P apps, but you can only run one of those apps at a time.