Ok well I had two completely different issues cause strange clicking like that. YMMV
1) On my ErgoDone some of the thumb keys made this noise and it drove me absolutely nuts. Neither lubing different parts of the stabilizer nor the band-aid mod helped. Eventually I realized the Acrylic case was flawed in having too little room between it's inner edges and the outer edges of some keys. In other words, the clicking turned out to be the sound of some keys hitting the acrylic case on the upstroke!
2) I had something really similar affect the spacebar on my Tex Yoda II. At first I tried different lube and silencing approaches, and nothing worked. Eventually I narrowed down the problem to the stabilizer itself. After close inspection, I realized one half of it was GMK and the other half must have been some other type of Cherry-style stabilizer. I re-installed it with both GMK halves and it no longer made that noise.
So maybe check to see if your plates bottom row is too close to the edge, possibly a defect caused by a misaligned jig during the machining process.
Also check if maybe the stabilizer needs replacing.
Good luck!