Could you tell me please how the assembler was rotated when it vanished?
Or do you mean the inactive Mai?
If you mean the inactive Mai: that is wanted that it vanishes. It is the robot itself, where you just add some missing components and the program. 
It was the AI assembly table itself that was vanishing - I built a MAI, then added the bill to activate it, and as soon as MAI came to life the table vamooshed, I think however the problem
may of arisen after I updated to your latest build - I just deleted the old MAI + MISC folders, and unpacked the latest version, perhaps something therein caused the issue (is it a good idea to do that by the way? Update to newer mod versions on a active colony? Perhaps it's safer / wiser to wait until a new colony is started, so everything is fresh? I think I've answered my own question!). As for the rotation of the table, it was vertical, with the output circle where MAI appears once constructed on the western side of the AI table, hope that makes sense.