@Nicki,
Im a bit pushed for time on the project, so for now Im just sticking to the version I have, which doesnt offset the panels. Once I have some time, I will send strip away everything except NGUI and send it through.
The hierarchy is setup the same as follows:
Main NGUI object
anchors for each position (top left, top center, bottom middle, etc)
underneath each are a number of panels.
If I set the position of the main NGUI to 0,0,0.
the panels are in the correct places.
by default, the object is at 0,100,0, at this position the panels are much much higher than the NGUI object and the anchors.
Adding a new anchor and panel, causes the same issue, but only in 3.6.6