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.
On my system (Windows 7 64-Bit, Core i7 980X):
nanosTaken=4999902563 millisTaken=5001
System.nanoTime() uses OS-specific calls, so I expect that you are seeing a bug in your Windows/processor combination.