I use backgrounder to allow-disallow so I take it you are using something similar or same? It prevents apps from ever going to background state from closing unless specified, however the problem is some apps can fire up on their own so I take it you mean in regard to that situation. ie..mail app launches on own and runs in background whether I've run it or not and only leave process list if I actually run the app myself and close app, then it comes under backgrounder rules and must quit.
Not sure if there is a more permanent fix for total prevention unless you disable certain apps.....not ideal.