did you read the whole thread? you realize that it's only a problem on multi-core cpus? Sorry if you are talking about them, I got impression that you aren't.
When using System.nanoTime() on my computer with a single-core CPU, the game I wrote would suddenly pause for about half a second every once in a while (about once per level). When using the millisecond timer instead, this problem stopped.
So System.nanoTime() has problems on single-core processors (or at least on mine) as well. System.nanoTime() is evil.