Stuck Jiffies is a known bug in the 2.0 Beta 11 software. Since the bug is in the kernel, if you install the Hijack kernel, the bug will be fixed.

Stuck jiffies is when the player stops responding to inputs for 15-20 minutes yet keeps playing music.

This may or may not be your problem. Sounds more to me like a wiring issue or perhaps the negative spike bug. Have you looked at the Troubleshooting section of the FAQ?