Are you allowing it enough time to recharge? With alkaline batteries, my 5400hs takes ELEVEN SECONDS to reach a full charge (IF the flash output was maximum power). With my Quantum Turbo batteries, however, it only takes about 1.5 seconds at full power.
If you are shooting at 4 frames per second with relatively fast film (ISO 400) your flash does not need to put out much light to get the job done, HOWEVER you might be using 1/3 of the flash unit's power with shots 1,2, and 3 of a four frame burst leaving you NOTHING for shot number 4 of the sequence. If you do not shoot anything for 20 seconds or so, and then a single shot here and there your NEXT four frame burst could wind up (1)perfect, (2)perfect, (3)perfect, (4)no flash due to this power "problem." The sum total of this is that after 36 frames on a roll, you have three or four that didn't have flash. This is, of course, just a theory but it could be the cause. The BEST thing is that if I'm right there is no repair bill but you WILL have to shell out $450 for a Quantum Turbo battery, charger, and CL-5 connection cable. (I have two of the Turbos and they are GREAT).
I use 800si bodies and 5400hs flashes for weddings, and the exposures are DEAD ON every single time. I absolutely LOVE the consistency of the Maxxum system.