I tried to create a machine w/ that tool and only two blocks showed up on the json file. The rest didnt.

Modular machinery (latest version as of oct 24, 2018)
Pictures:

{ "parts": [ { "x": -1, "y": 0, "z": 1, "elements": [ "thermalfoundation:storage@1" ] }, { "x": 1, "y": -1, "z": 0, "elements": [ "thermalfoundation:storage@1" ] } ]}

Dont worry about that blue thing in the background. Thats just me goofing around :)

Sorry for the delay, is this still occurring? Sounds like a selection problem, personally. If you're still having issues using the tool, please come to the mod's discord and post into the channel for modular machinery.