Atmel AVR ADC Inconsistent Sampling Time
The inconsistency isn't periodical as you say, looks more like random.

ISV vector or compare have some limitations when a call is break by an incorrect memory assignment. I assume that is function from the Watchdog, but could that be random triggered with so little calls?

One sample is periodically disappearing due probably a incorrect flag setting or a exited interrupt function during the ISR ON cycle.

This may be due hardware interrupts may be triggered and stopped from the internal scheduler or a periodic bug in the MCU produced by the load itself.

Eventually some inconsistent ISR timing setting may produce this kind of failure.