Have tried to tune it without the aid of the ATU but the SWR is right off the scale.
I have the antenna on a mag mount, which I now found out Diamond do not recommend!
What I have to do is get a good earth run from the thread on the SO-239 to an earth bolt somewhere on the vehicle before I start chopping.
I wish you'd mentioned that first. I assumed you were just using the ATU to give you a bit more bandwidth. Forget everything I've said. Depending on the mismatch and the power you've been running you may have actually damaged the coil in the antenna forcing it to work with an ATU.
OK, assuming the antenna is OK then back to the problem at hand.
You basically have half an antenna. A magmount isn't going to provide enough capacitive coupling and neither is running a bit of wire from the thread to a bolt. Remember RF runs over the skin of the conductor so you're going to need to use something with a large surface area so flattened out braid from RG213 should be considered the minimum but again, it isn't really sorting the problem.
If you want it to work well you need to consider drilling a hole in the car and putting a permanent 3/8 mount in or at the very least using a lip mount such as a Diamond K400 with screws that bite through the paint to the metal below.
Please read this section of the K0BG.com website about mounts. http://www.k0bg.com/antmount.html
Also have a read through other sections on the website especially in regards to bonding etc.http://www.k0bg.com/
Until you've sorted out a better mounting and grounding solution all you'll be doing with anything you try to do to sort it out is chasing yourself round in circles.
You can "get away" with using a triple magmount on 20m and above. You can get away with using a single magmount on 10m. You can't get away with using a magmount at all on 40m without some problems even with 10W and definitely not on 80m.