Have you looked in the generated g-Code? Is it actually there on layer change?
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I tried a different tower from the prusa website, with similar Gcode (but not identical) for layer change, and that worked just fine. So I'm thinking something is messed up in the code example of the other.
Again, look in the generated g-Code. Just open it with a normal text editor and search for the Z value where you expect a change. See if it is there.