More on the "copy" bug: It seems to affect (mostly, but I just had one time it affected me with no connectors) the connectors. I can reproduce it by chaining several in a row, copy to another CraftoMate, and then disconnect any of the lines connecting the connectors in the source or target Craftomate. If you go back to the other CraftoMate, the same line is broken.
Another update: Further experimentation seems to point not at the connectors themselves, but the connecting _lines_ between program elements (I mainly noticed it with connectors because I would place two connectors in a row, and then "break them" to cause the program to stop at a known point).