Just a quick update on whats happening,
Lens went off to Canon, they tinkered with the lens alignment and replaced the IS unit. Took about two weeks, it was much improved. However, still not brilliant. (It at least didnt blur it at 1/40th at 24mm anymore!) Had it for a couple of weeks before deciding something still wasnt right and that my photos should be sharper so i went back to the camera store.
At the store we tried many many things, different bodies, different lenses and we found a few things out.
Their old, second hand 24-105's IS works much better than ANY of their new 24-105's IS.
IS works much much more effectively (about 1 stop better) in One Shot AF mode than AI Servo, we noticed this across multiple 5D3s and multiple copies of the 24-105 however, we only tried this with their new lenses not their second hand one. This was even noticeable on bodies such as mine where I use BBF, the AF mode dictated how effective IS was even if AF wasnt being used when taking the photo. I have not been able to replicate this effect on my 70-200.
We then sent an email off to Canon explaining what we found and the store will call me when they get a response.
And Pepeto2001, I tried that and got much better photos, but if I'm gonna have to do that for photos with an exposure longer than about 1/12s, its really just an annoyance.