Thanks to the OP for posting this! I have had the same issue and it just started yesterday after I updated about 30 apps at once... (was troubleshooting a different issue which caused the play store to stop working).
Music skips for me when the screen is off with all audio; the apps I've tried are Soundcloud, Stitcher, UberHype, Play Music, the samsung music player, and N7. Whatever the issue is it slows down the phone significantly too when I wake the device. I'm using model SGH-T889 (T-mobile) running 4.1.1.