I have few Atomic user that are using Vista and emumovies they don't have this kind of issue. But , in fact, i don't know if there are in Vista 64 mode or vista 32.
If i prepare you a "ready to test" version of Atomic .(you won't have setup to do , just unzip and run the exe) , could try on Vista 64, to see if the same probleme occurs? Could help to determine if it is a vista issue or else.