It fires two spark plugs at the same time. One on the power stoke, one on the exhaust stroke. The cylinder with compression/less resistance gets the majority of the spark. Cylinders 1&6, 2&5, and 3&4 are the pairs fired together. While I haven't had it happen to me personally, if there is something in cylinder #3 that is easier to fire than on #4 the majority of the spark could go to #3. In theory at least.
What do the spark plugs look like?
Have you checked the cam sensor synch?
Check wiring to the injectors too.