are you sure the click is not happening as the sequencer cycles around, rather than randomly?
I have noticed this behaviour when trying to make drones (although less so with melodic sequences) and, unfortunately, have not found a way around it. I have tried everything and it still clicks as the sequence cycles around. I end up recording to audio and removing the clicks manually if they're really noticeable.
Having said that though, I haven't really noticed it with melodic sequences.
If it is completely random, it may not be the sequencer at all.. more of an envelope issue. Have you tried rolling off a little bit of attack on the amp envelope? Also try using wave reset for the oscillator(s) and see if this makes a difference.