Hmmm, well .. for the games that no longer have the "ok" prompt screen, these games were already played (that screen only comes on the first time you load a rom), as for the "loading, decrypting" screens still showing, are you certain you applied the .diff patch before compiling?
Another thing is maybe the version of MAME you have (.123) doesn't have the option to remove those screens with the custom .diff ... I know my .110 version still shows these screens, but my .128 version does not.