Strange, didnt had a problem at all with SW Trilogy, but yes. I can confirm that Bart was using an...updated? rom for Daytona 2 so that's why It doesnt works with our roms, Daytona 2 PE works perfectly though. Just enter the test menu (with number 6 on the kb) and then change the link to single mode on the game config. Its just a common thing for a Twin Cabinet game.
GraphicArts: Are you sure that you're in the same folder that the game is? Remember, you should be using Chain Directory's. I recommend going to the emulator root and then placing the roms in a folder inside there.