I hope my speculation here is wrong (probably), but...
I've recenly been re-editing the SSLate Old Zep kit for SD3 and have found similiar problems on occassions with the snare. My suspicion is (and at some point soon I'll confirm it) that some of the samples have not been properly edited at the very beginning of the samples (values are not exactly zero) so as one sample blends into another it leaves a small click. Generally it shouldn't matter but it appears the samples are not properly "cross-fading" into each other, so to speak, possibly as a result of how the samples are programmed or how the player deals with the samples. In Kontakt it may be adjustable so you may be able to solve the problem that way - I'm more familiar with Battery but I'll see if I can find the specific adjustment.
Part of my suspicion also relates to the sporadic behaviour - most likely there are multiple samples in the velocity range so if several kicks occur close together it will cycle between different samples as repeating a single sample over and over can sound mechanical. This would explain why the issue occurs intermittently - only one sample contains a flaw.
Sadly it's not always an easy issue to isolate. What you could do is this: first check the velocity of the MIDI notes triiggering the kick when it clicks. Check in Kontakt to see which sample names are assigned to that velocity level. Open the samples in a wave editor and carefully check them out.
I'd also do what Linear suggested and try a different kick or kit to see if the same thing occurs.
But before you go crazy I'd bypass every single effect after Kontakt and see if the click still occurs. Then start re-engaging the effects one at a time and checking after each to see if one of the effects is an issue.
Occassionally I find the metering in Sonar doesn't seem to respond fast enough to find really fast transients whereas they are visible in Waves Dorrough meter plugin.