First off thanks all for any help and input so far, even if I'm not getting anywhere i appreciate people giving up their time to help. Unfortunately that is just where I'm getting, no where.
@Phaedrux The filament is fine it can easily unspool straight into the extruder, I have tried multiple seam alignments from aligned to random, along with multiple slicers (cura and prusa). The bed on the sapphire plus is supported on two edges so is much more rigid than a lot of Chinese coreXY machines and the bed level screws are down tight enough it does not really move around.
@lodger Yes it is the BMG clone that is shipped with it however I have also tried a titan extruder I had kicking about with no change.
As stated at the beginning this has been happening on two machines for me now, with the exact same issue, and both machines had been working fine before the duet. I "upgraded" the first with the duet because of the questionable saftey of the first machines electronics, and the second because I already had the duet so why would i not? However the fact they have both worked fine without it rules out it being a mechanical issue, there is no way it is z wobble, or a bad extruder, snagging filament etc because they have all been proven to work fine.
over the last few days i have tried, in no particular order, multiple filaments, multiple extruders, extruder tensions, changing jerk settings both higher and lower, changing acceleration settings both higher and lower, different temperature ranges, retraction settings, pressure advance settings, I have moved all of the motors around onto different drivers, checked belt tensions really anything that could produce banding on the Z axis like I'm getting that I could think of. It is not layer shifting as the bands appear the whole way around the prints rather than sticking out one side and in the other.
I have tried every suggestion everyone has made on the forums, one at a time and done a test print in between nothing has made any real improvements.

the above imagine is of two cubes printed back to back. The only difference between them is the worse one on the left was sliced at .1mm layer height, while the other at was .2 all other settings stayed the same.
The only thing i can see being wrong at this point is there is something wrong with my board. I just wish i had a second one kicking about i could swap to and stick the SD card in because that would prove it one way or the other. At this point I'm getting close to just tearing the duet back out and converting it back over to the makerbase board that it came with.