Se RANDOM_DELAY estiver definido no seu /etc/anacrontab , é o comportamento esperado.
Cópia completa da página de manual anacrontab(5) :
If the RANDOM_DELAY environment variable is set, then a random value between 0 and RANDOM_DELAY minutes will be added to the start up delay of the jobs. For example a RANDOM_DELAY set to 12 would therefore add, randomly, between 0 and 12 minutes to the user defined delay.
Isso pode explicar seus sintomas.