Does any one know the spec's for the various crystals on the DUE?
I wrote a little sketch (rtt.ino in the git link below) that checks the 32KHz crystal against an NTP host over the serial connection. I set the prescaler to 32 to get 1024 interrupts (ticks) per second (see Ch. 15) from the RTC/RTT crystal. The only magic required was that you have to disable the interrupt in the ISR and wait for RTT_SR to clear before re-enabling the interrupt and exiting the ISR. Frequency data is requested by the NTP host every 10 seconds or so, and after many minutes, the crystal frequency appears to be within 3ppm of the NTP-disciplined frequency on the Linux host (probably accurate to less than 1 ppm). The sketch has an option to measure the RTC/RTT crystal against micros() on the DUE.
Frequency offsets for other MCU's, RTC's and RC oscillators are in crystals.txt on the git link below.