I have just bought a meteor65 pro for my first quad and got it to bind with my Tx16s controller. Straight out of the box it won't fly, it instantly flips and looking at the motors in betaflight it appear that one of them runs away given the slightest throttle and won't come down. Any idea how to fix it?     

Send it back and ask for a replacement.

Don't touch anything on it or mess with anything. The fault you are describing shouldn't be happening on a brand new quad.

Although a brand new BNF should fly correctly out of the box, the return process could be a hassle or take a long time depending on where you purchased it. Sometimes it might be worth some quick diagnosing to see what is the problem, and maybe the shop you purchased from will ask you to do the same.

The screenshot you posted, is that from the blackbox log? When one motor command runs to 100% just trying to take off suggests that motor is not giving enough thrust. Motor 2 is front right, you can check the prop is installed properly, not loose on the shaft, motor spinning smoothly, and motor plug is secure. You can also connect to BF using the motors tab to spin up motors one by one, then you can see if each motor is spinning smoothly. Also make sure nothing is caught on take off, for example if the battery lead is rubbing against the ground sometimes that is enough to block the drone, you can hold it in your hand if you are comfortable when you arm it for a quick check, leaving your finger on the disarm switch.

I have it down that either one of the motors is broken or the ESC is broken. Neither problem is easily fixable by the OP. Yes it could be a prop issue, but this is a quad that has never flown, a brand new BNF. The second you start messing with it, the chance of the supplier claiming you voided the warranty tends to get higher. Hence send it back.

At the very least, open a ticket with the supplier and let them know it is broken.

If you really want to troubleshoot, the props are definitely one place to look at. Ascertain whether they are spinning in the right direction. Running props in/out incorrectly will often result in a quad flipping over on arm. If they are set wrong, then swap that option in Betaflight so they spin correctly.

If on the other hand you have one motor that doesn't spin as fast as the others, it's either the motor or the ESC (or maybe both). Replacement is the only fix for this. You will be able to tell pretty quickly if it is this, by spinning up the motor manually in Betaflight, with the prop on, but only start it up to the point it is smoothly spinning. If you do this for each motor, but one of them seems to be spinning awkwardly or twitching, then you have a more serious problem. You could check to see if the motor connector is fully pushed in, for starters. Then try moving that motor to a different connector on the FC. if it moves smoothly on a different connector, the ESC is broken, If the motor still acts weird, but the motor plugged into it before was fine, then the motor is broken in some way.

If you spin the motor(s) in Betaflight, do only one motor at a time, and hold on to the quad with your hand. Do not set it down for this. Go VERY easy with the slider to see which way the motor spins and how it behaves.

Yes, like very little on the slider is needed to get a motor to spin. You just want that point where it spins without twitching. No 100% throttle.

Also never do this spinning motors with the props on with anything over around 2.5". I will test motors with props on, on a 3S 2.5 inch build. But caveats. I use a 2S battery for the test and I have done this many times so I know the dangers and everything else that might happen.

If I bought it locally I'd send it back. If it came from China... I would do a little more troubleshooting. If motors have plugs it may be useful unplugging and pluggin them back. I once crashed a tinywhoop and it looked perfectly fine, but the moment I tried taking off it would disarm claiming runaway. Unplugging/replugging motors fixed it.

Also if one motor wasn't spinning the same in BF configurator motors tab I would try swapping it with another one. If the problem went with the motor, it is a motor issue, if the problem stayed in the same place it is the ESC, If two motors are dead now it is probably a short that killed the ESC. The first option can be resolved by having a new motor sent by the seller, anything else I'd send the quad back.

If you have another AIO going spare, try plugging all the motors into it and seeing if they spin ok on a different AIO. That would be one of my first suggestions. If they work fine and the quad flies, then you ruled out the motors. If you have a second set of motors, try those on the (possibly) dodgy M65 AIO and see if it flies ok? If it does, well I'm stumped. If it doesn't, well you probably have ESC woes.

It helps that you are experienced and have flown and presumably have some clue how to troubleshoot quads with issues.