Also having the same problem with 5 nanites factories and 6 assemblers. 1 master assembler (cooperative mode unselected). and 5 slaves (cooperative mode selected). Only one nanite factory set to "use assembler". Only the "master assembler" have the "nanite factory queuing" selected.

Tryed with only one assembler set to nanite queuing with only one nanite factory set to use assembler and did the same. Tryed to set all nanite factories to use assembler with one assembler set to nanite queuing and did the same. Looks like when you set one nanite factory to use assembler, the other 4 queus reguardless of the use assembler setting is selected or not.

i am also having massive queues with only 1 nanite control regardless of amount of assemblers it queues a MASSIVE amount of items which i end up having to salvage back down :|
might only be happening when i use a beacon to build another grid object