The New Year is dawning and with it a new BuzzTunes contest!

Pesticide, if you're talking about the click when transitioning directly from one note to another with no note-off in between, that's simply the result of the waveform not being at zero at the end of the first note, then jumping to zero when you trigger the second note. It can be avoided in a couple of ways. 

First, you can use tone portamento (effect 03 XX) to continue playing the waveform of the first note but sliding the pitch to the new note. Using, for example, 03 FF will give you a very fast, almost unnoticeable slide. If you use very low values like, say, 03 01, you will get a much slower slide, but in order to reach the note that you're aiming for, you may need to continue the effect in subsequent lines of the pattern (just 03 with nothing in the effect argument column will work fine) until the target note is reached.

Second, if you're using Matilde 3, you have the ability to use virtual channels, to fade out the old note whenever a new note is triggered on the same track. You need to set the virtual channels attribute to 1 for a particular instance of an MTrk machine (in the machine view) and also define a volume envelope for that machine (in the wavetable view) with a sustain point followed by a decay for this to work. Using an attack and a decay of the same length will eliminate any popping sounds, but if either the attack or decay is too fast, there may be some scratchy artifacts at the note transitions (as Buzz apparently handles those volume envelopes very coarsely).

If you are talking about the click that happens at the loop point (small click that repeats every second or so), that can be eliminated by setting the loop end point to 44100 in the wavetable view.

I can't tell what would cause the track to fade out. Perhaps looping is turned off in the wavetable parameters, or you have an envelope set without a sustain point?

As for the track staying silent, that may have to do with the 03 effect itself. If a note is not already playing in a track when you use the tone portamento effect, it will have nothing to slide from, so the track will remain silent. You should be able to get notes in those tracks to play again if you trigger them without the 03. And you can do this safely without clicking, because if a track is already silent when a new note is triggered, then it won't click anyway.