Do you have the deb or the flo?
What are you using to identify which apps are running in the background (i.e. an app)?
If it's not a rogue application or wakelock, I would probably try flashing a different kernel and test it out for a couple days. If your problem persists, I would flash stock and use it for a week. I always recommend flashing to stock so you can get a reliable baseline to compare it too. If you are on stock and still exhibit the same problem, I would play the warranty card.
That's at least what I would do.