You will need the 10nF caps in addition to the level converters. The parallel resistors work with the hall-based encoders that are specific to the motors from the kit. There are noise spikes all over the encoder lines (because the cables are really long, not twisted, and high-impedance) that the Due will pick up due to its speed and i/o sensitivities. Without the caps you will have positioning errors. I struggled with this for a few hours until I busted out the scope and looked. Once the caps were added, no more errors.