I can assure you that NETBIOS is not required for a Server Engine.
Suggestion: Try a command like this (with your own servername, of course):
TELNET <servername> 3351
You should get a blank screen, letting you know that the connection succeeded. If this works, then you should have valid connectivity. You can also try testing with the Function Executor (WBEXEC32) to open a file on the server -- it should succeed. If these fail, then you will need to fix the network routing, first.
All of the registry settings can be found in HKLM/Software/Pervasive Software. Look in the Communications Requester group for the Supported Protocols and change it to TCPIP.