Ok, you are using a plug'n play module it is why.
So , run AtomicManager.exe
Click on "Load config"
Select the file <atomicfe>\plugnplay\arcade_simple\arcades.cfg
Go on the option tab, and tick the options you want.
Click save.
And try again.
It is because when Atomic is in plug'n play mode, it ignores the start up config. It starts on plug'n play configs.
For the .bat , right click on the link , choose "save target as" , save it on AtomicFE folder , double clique on the file , then the file should be generated in the Atomic folder. But anyway , i don't need it for now.