I'm not sure why that's happening. Your settings file looks fine. I tested beta 9 myself and I don't have that issue. All I can figure is that maybe LaunchBox isn't recognizing the platform as a ROM-based platform, and thus not offering to delete the ROM? Four criteria have to be met in order for LaunchBox to prompt to delete the ROM:
The "Allow Deleting ROM Files" setting needs to be checked (and it is in your settings file)
The "Application Path" in the game needs to not be empty
The game must have an emulator associated with it
The ROM file must exist
I'm assuming at least one of those criteria are not met. It's also possible that it's a file permissions issue and LaunchBox doesn't have access to the file, for one reason or another.