A method for synthesizing with a template-free polymerase a plurality of polynucleotides each with a predetermined sequence, wherein the template-free polymerase has reduced coupling efficiency at one or more inefficiency motifs, the method comprising the steps of: (a) providing a reaction chamber for each polynucleotide of the plurality, each reaction chamber having disposed therein a synthesis support with initiators attached, wherein each initiator has a free 3'-hydroxyl, and wherein each reaction chamber has an inlet and an outlet and a filter that retains the synthesis support and that is operationally associated with the outlet so that reaction solutions exiting the reaction chamber pass through the filter; (b) providing a waste manifold operationally associated with the outlets of the reaction chambers so that whenever a positive pressure differential is created between the reaction chambers and the waste manifold reaction solutions are removed from the reaction chambers; (c) repeating for each reaction chamber, until a polynucleotide of such reaction chamber is complete, cycles of the following reaction steps: (i) contacting in a coupling solution the initiator or deprotected elongated fragments with a 3'-protected nucleoside triphosphate and a template-free polymerase so that initiators or deprotected elongated fragments are elongated by the 3'-protected nucleoside triphosphate to form 3'-protected elongated fragments, (ii) deprotecting the 3'-protected elongated fragments with a deprotection solution, and (iii) applying a pressure differential between the reaction chambers and the waste manifold to remove reaction solution(s) from the reaction chambers; wherein the kind of 3'-protected nucleoside triphosphate contacted in step (i) in a reaction chamber is determined by the polynucleotide sequence of the reaction chamber, and wherein, prior to each cycle, one or more short cycles of step (i) is carried out in a reaction chamber whenever an inefficiency motif is present at a 3' end of a deprotected elongated fragment of such reaction chamber. (a) providing a reaction chamber for each polynucleotide of the plurality, each reaction chamber having disposed therein a synthesis support with initiators attached, wherein each initiator has a free 3'-hydroxyl, and wherein each reaction chamber has an inlet and an outlet and a filter that retains the synthesis support and that is operationally associated with the outlet so that reaction solutions exiting the reaction chamber pass through the filter; (b) providing a waste manifold operationally associated with the outlets of the reaction chambers so that whenever a positive pressure differential is created between the reaction chambers and the waste manifold reaction solutions are removed from the reaction chambers; (c) repeating for each reaction chamber, until a polynucleotide of such reaction chamber is complete, cycles of the following reaction steps: (i) contacting in a coupling solution the initiator or deprotected elongated fragments with a 3'-protected nucleoside triphosphate and a template-free polymerase so that initiators or deprotected elongated fragments are elongated by the 3'-protected nucleoside triphosphate to form 3'-protected elongated fragments, (ii) deprotecting the 3'-protected elongated fragments with a deprotection solution, and (iii) applying a pressure differential between the reaction chambers and the waste manifold to remove reaction solution(s) from the reaction chambers; wherein the kind of 3'-protected nucleoside triphosphate contacted in step (i) in a reaction chamber is determined by the polynucleotide sequence of the reaction chamber, and wherein, prior to each cycle, one or more short cycles of step (i) is carried out in a reaction chamber whenever an inefficiency motif is present at a 3' end of a deprotected elongated fragment of such reaction chamber.