Another update,

I found this discussion on the makers website. It seems to be the same problem I have exactly and it all points to things not being as they should be it by manufacturing or assembly issues. The bottom line is I need to make sure the machine is perfectly level and also that all the parts are flat and haven't been distorted by any fasteners and then re-square my towers and start over again basically - but it will be well worth it.

I happen to have a number of adjustable M6 threaded feet so will probably encapsulate 1 or 2 M6 nuts on the inside of the base, perhaps 3D print a holder and fasten it using the 2 standard holes and fit the 3 or 6 adjustable feet with an extra M6 nut on the external/foot side to lock once levelled.

While the machine is in bits I'll mark 3 points on my desk with tape or something where each of the feet will stand for reference and keep the printer in one place. I will level the bottom of the base without the top on. I will then check when the base is assembled that the top of the base is level and thus is parallel to the bottom of the base (and double check the bottom of the base is still level and sitting on the designated marked spots on the desk)

I will then check the insulating board which the ONYX sits on (aka the Spider?) is also level once installed and flat - and that the ONYX HB and Glass build plate are also flat and level once fitted.

With all that work, naturally it's back to square one with set-up, final tightening and calibration (or hopefully "a" square one should I say....... no? no, I shouldn't say - because that's a terrible joke...)

Once things are physically fit further measures can be taken to help the machine make the absolute most of what it's got to work with. These steps by the sounds of it will modify the "perfect" set of calculations that are used to coordinate the movements of a "theoretically perfect" Delta printer to better suit your not so perfect real world machine as best is possible - ultimately distorting parts as they print to fit the build plate - if the bed really is warped, I would guess it will print warped parts, if the bed is flat and the machine is warped, then it should print flat parts (I think?)

The tool is called OpenDACT and it will only work on Repitier machines as far as the good people on that thread suggest. Its obviously only for Delta Printers.....

http://forum.seemecnc.com/viewtopic.php?f=77&t=9090