Just a quick update, I have successfully fixed "the error of my ways". I have been through the model (of 340 components) and removed all instance names and corrected the definition names. I worked through it methodically and was able to take advantage of the "component-ness".
It ended up being a fairly simple task, despite the first thought of going back through it
The outliner is all neat and tidy, bounding boxes tightly fit and Cutlist is reporting the correct names and sizes(hooray).
I know why I've been getting odd results now, it's easy when you know how! I'm very meticulous about how I go about things, just been going about it the wrong way. I'll put it down as "experience".
Thanks Dave, simple solution but a very valuable lesson learned, onwards and upwards
No. It wasn't in your "top ten" anyway!