AT91SAM3U main clock doesnt appear to be starting

I am messing with the example code from Atmel for the AT91SAM3U-EK and every application I load gets stuck right here in the low level init function:

while (!(AT91C_BASE_PMC->PMC_SR & AT91C_PMC_MOSCSELS) && (timeout++ < CLOCK_TIMEOUT));

Anyone have a clue? These projects worked before I updated YAGARTO.