I'm having the same problem with deconstruction. I tried to build a ship cemetery where i send captured ships for scavenging There are two nanite factories with deconstruction upgrades. It seems that when two factories end up targeting the same block for a stream, they both cancel the action and call back their nanites. If only one control factory is enabled, it works as expected.
Until this is patched, the solution would be to space Nanites Factories enough so they don't conflict with each other before the very end of the construction / deconstruction, and then disable all of them except one.

Erratum, turns out it was an Uranium shortage.

I don't want to jinx it, but it seems distance from the factories was the issue. I've got two of them near the structure i want to build and it works like a charm!

I'm thinking has to do with syncing properly on distance from player

I'll try to film it and put it on YouTube.

Videos will finish uploading in a few hours and will be here: https://youtu.be/yzCkF3Axssg

In this video, nanite factories ignored a ship until I put a deconstruct beacon on it:
https://youtu.be/lKuBTPV30I0?t=10m44s
And on several occasions, stopped working for a small amount of time.

I find that when the control column or w/e you call it goes up and down without doing anything, the solution is to simply empty that nanite factory of all its materials, and it works again after it sucks them in again