Myself and another developer on my time recently moved from a Core 2 Duo machine at work to a new Core 2 Quad 9505; both running Windows XP SP3 32-bit with JDK 1.6.0_18.
The problem was resolved (with some open suspicions about the suitability of nanoTime() on multi-core systems!) by adding /usepmtimer to the end of my C:\boot.ini string; forcing Windows to use the Power Management timer rather than the TSC. It's an open question as to why I needed to do this given I'm on XP SP3, as I understood that this was the default, however perhaps it was due to the manner in which my machine was patched to SP3.