Thanks again.
I tried soldering on a watch crystal by itself and it is not enough - in fact it is worse, only 42 seconds per minute! With capacitors it runs at a more conventional 60 seconds per minute
But there is no easy place to solder the capacitors on (I was literally holding them between the crystal and the shielding of the USB port, which can't have helped the accuracy much).
Capacitors are really really important for the Crystal to work proper, they needed that the main frequenz of the Crystal swing. On page 1407 of the full SAM3xa is an formel to choose the right value.