1. Clicking when the audio engine switches from the "live" feed to the "loop" feed and back when in duck mode. This was caused by the audio engine switching streams at something other than zero crossings. A very quick fade (on the order of a millisecond or two) on the in and out of the "live" feed solved this problem. FIXED.
2. Clicking in the looping engine itself, caused by loops that are cut at something other than zero crossing points. Apparent in mix mode, but obvious in duck and send. This was solved by recording a very quick fade at the beginning and ending of loops as they are recorded. (There was already one on the beginning; we just put one on the end.) FIXED.
3. Clicking when audio first enters a filter, and that filter is anything but wide open. This occurs in all three modes. We haven't figured out why this is happening yet. FIXED, sort of. We got the filter popping fixed, but Replicant Whack-A-Mole means that we created a new problem with this. Whee.
4. Clicking when the following conditions occur: loop length is set to anything larger than 1/16, and a retrigger occurs mid-loop. Say you have triggers on steps one and three, and the loop length is set to 1/4 note. Obviously, step three is only 1/8th note, or half of the desired loop length. So the loop will only play half-way before getting retriggered. Thus it isn't able to play the fade-out that was recorded to fix the clicks in instance #2, noted above. This one is the biggest bear of all, and we're not sure how to address it, as in order to play a crossfade, the plugin would have to know that a random trigger is going to occur on a given step. In normal programming, this click can easily be avoided. But when you're using heavy randomization of the loop length, and the sequencer mode is set to "retrigger," you get a lot of these.
So, here's what we're going to do: we're going to release an update shortly that has the first and second instances (which are currently unavoidable) fixed, but not the third and fourth (which are more or less avoidable, except in certain circumstances.) We'll continue working on this exclusively, and release another update when we have fixed the third and fourth instances.
As I mentioned on KvR, we designed this plugin with drum slicing in mind, and it didn't really occur to us that it would see such heavy use on other material. We didn't rush the release of this product; we don't rush any of our products. We release them when we feel they do what we want them to; Replicant is perfectly capable of slicing straight-time drum loops ad nauseum, and you'll never hear a click that will be more apparent than the program material. Using it on sustained material is certainly feasible in its current state, but you have to remember that it is, as I've mentioned previously, like drying your cat in the microwave. It _can_ do it, but it isn't very good at it. The final revision will basically have the entire looping engine re-written to allow it to excel at slicing sustained material, so the cat will dry un-harmed.