I recently built a 3.5.7 kernel for my EP9302 ARM board (a Technologic Systems 7350) and now the timing is very inconsistent. I built the kernel with HZ set to 1000 so usleep(1000) should give me 1 millisecond sleeps (Okay, in practice a 3.0.4 kernel needed usleep(948)) but when I try to verify the timing by looking at Timer 4 on the processor, it's sleeping twice as long as it should be and it varies by as much as 50% on successive sleeps. I see the same behavior on ITIMER_REAL. Very inconsistent.

Any ideas what I may have done wrong in building the kernel? Does using uClibC versus glibc have any bearing on this?