Erik will probably supply you with the "bible" (or search for "bible" on this site); you will find details on timers operation as well as on "jitter" (which is called interrupt latency (in the "bible" they called it "response time")) there.

You can use the current value of timer at the moment of reloading the timer to compensate for the variable latency. For example see Peter Dannegger's examples on his pages.

Jan Waclawek