Answer:
Cooking times for a soft boiled egg (and getting it just right) depend on a several factors: (i) the storage temperature of the eggs, (ii) the size of the eggs and (iii) [believe it or not] your elevation above sea level. However the temperature of the egg in the first place matters the most.
As a general rule, the cooking time for the "perfect soft boiled" (soft runny yoke and firm white) is 5 to 6 minutes. To get around the vagaries, try the following:
1. Piece the larger end of the eggs with a skewer (only just breaking through the shell). This will stop the egg-shell cracking while cooking.
2. Place the eggs in a saucepan of water ensuring the eggs are covered with water.
3. Over a medium heat, gently bring the water to boiling point - watching closely for the first signs that the water in boiling (bubbles rising more or less evenly throughout the water).
4. Maintain at boiling for 3 to 4 minutes.
5. Remove eggs from water and allow one minute to rest before serving.