the interval time between updates on egg hatching and buddy system is 5 minutes. every 5 mins to the second the buddy system will add on the last clocked distance.
I am still figuring out exactly how long between each location check that adds the distance but for it adding to your buddy/egg it is 5 minutes. if you get a loading circle at the 5 minute mark it will delay the add up until the loading is done, giving the impression the next one is shorter but it still keeps to the 5 min mark.
the counter starts the moment the game has finished loading. If the game loads, and the character is displayed at XX:37, this counts as the first location marker, 5 minutes from then, XX:42 it will add the next totalled distance to the buddy, and XX:47; XX:52 and so on
don't forget the most effective way to clock distance is to walk in a straight line. the game checks your location at certain intervals, draws a straight line between them and uses that as a distance (if you travel to fast between two points it thinks your driving - so no switching between apps or staying too long in the caught pokemon screen).
i.e. walking in a straight line for 1 km will clock 1km in distance; walking in a 1km circle will only clock about 600m as it only clocks a triangle between 3 points rather than your actual path taken.
I usually walk 1km in a straight line, wait for the distance to be clocked in the buddy and turn around 180degrees and walk back 1km. doing this and checking my distance I have clocked 2km.
if you do need to make a 90degree turn or more I would advise waiting for the buddy to clock the distance before carring on as you would have walked more than what has been clocked.