I have the same problem here, and I guess the filter doesn't have time to get into auto-oscillation between the p-locked sound and the bassdrum on the track... juste an idea, if you use the filter to get the kick, of course.
Other possibility : when I add some noise to the kick (self oscillating filter) to get some more "accoustic" sound, the behaviour is quite random, and 1 kick every 5 to 8 trigs is dampen on a 4/4 bar. Does it come from the randomness of the noise ?
Finally, sometimes when I add a triangle osc to the kick, it's also random, but I think this is caused by a phase cancellation, and depending on the frequencies of the filter and osc signal, you can tweak it to get it right.
My two cents
