Two things:
1. Make sure that the screen lock sound isn't enabled. On flashing a new rom, sometimes I'll forget to disable it and since I can't hear it or maybe it doesn't sound, especially when playing music, it'll almost definitely cause the stutter. Otherwise...
2. Like maschiosoosai said, turning up the clock speed will stop the problem altogether. If your kernel supports it, the "screen off max" frequency is the one you'd want to change first. I've found that around 700MHz (clock speeds vary by kernel) the problem goes from every time to about 50% of the time, and around 900MHz it's gone entirely. It's worth a shot, but you really have to be aware of processes keeping your phone awake and eating up your precious battery life if you choose this as a solution.
Honestly, I've found that my personal favorite solution is to not use my device when I'm listening to music. It keeps my battery going longer, and with my battery as used up as it is, it needs all the help it can get
