Can you do the following:
1. Find a game that you get this error with, then right click that game in LaunchBox and select "Edit" to bring up the Edit Game window. Then check the application path of that game and make sure the file exists in that location
2. Make sure you don't have an emulator set for some reason on that game
3. Make sure if using the default DOSBox that you a \\LaunchBox\ThirdParty\DOSBox\ folder and that there are files in it.