+1 on the charge of the battery if it is not high enough you can get this behavior as the coil is not fully powered when it is triggered.
Also check your coils for cracks this can cause some spark strength issues as well especially if they crack by just one of the outputs.
With the Stock coils you can also disconnect the plug wires cut off a half inch or so and reseat them this will help if the ends are corroded just make sure you hit it with some dielectric grease.