Wait a second!! Here! I have Subway alright. So you are saying my Subway is causing compatibility issue with WHDLOAD? How do I fix this issue and still have subway, thanks in advance?
It has to do with hardware interrupts. USB and network cards send them out and the custom hardware-banging nature of WHDLoad can't handle them. Just take Poseidon and your TCP/IP stack offline before running something in WHDLoad. If I'm not mistaken, the current WHDLoad includes scripts to do just that automatically when you start a game, and to bring them back online when the game quits.
Make sure those scripts are enabled in S:WHDLoad.prefs (and make sure you have them and that the right commands are in them!).