Focus issues Canon 500mm F4 L IS MKI

Hi Folks

I just recently picked up a Canon 500mm F4 MKI, i bought it used from a good friend of mine who takes very good care of his equipment. I know that i have a learning curve ahead of me with this lens, i have been shooting for about 8yrs now so not new but still always willing to learn. So here is my problem i have used the 500mm on both of my cameras 6D&7D on tripod or rested on a car window so pretty stable platforms, the 500 is quick but it leaves me baffled as to why the focus indicator in camera says it is focused and i take a series of pics only to find out that they are all soft with no detail Mushy if i can say that with single point focus or any combination of focus modes and drive speeds,of a stationary object i.e:Sled Dogs lying down etc etc,nothing super fast or fast movements at all most photos are taken at 1/1250 or above F8 down to F4 low iso, ETTR and all pics are Mushy but than can go out the next day and be spot on 8 out of 10x so i am asking if it is maybe Due to Contrast levels atmospheric levels, etc etc my Tripod is a Manfrotto 055XB Pro and a Manfrotto 804 head but i have a JoBu Gimbal on the way :). Remember we live in the Arctic so we have a lot of White here right now just to keep that in mind. See attached photos they are cropped a lot just so that you can see what i am talking about pic number 2 is sharpish and taken on a different day when the focus seemed to work.
Thanks
 

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I have read elsewhere that shooting out of a warm car window or open building door doesn't work so well when it is cold outside due to atmospheric disturbances from the warm air. It will mess up your images.

Having the camera and lens at or very near the outdoor ambient temperature would probably help.

Lastly, have you checked to see if the lens is focusing properly? It may need some tweaking (AFMA). There is a quick and easy method outlined here: http://www.fredmiranda.com/forum/topic/1354369
 
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Thanks Danski0224

I have tried the AFMA just with the batteries set up :P in the house so not optimal as it is not big enough for the 50 x focal length but from what I have done it seems to be spot on at 0 on both cameras. But you may be onto something with the ambient temperatures of the lens but even when I am out for awhile taking photos of the moon on 10 sec timer tripod and remote release with the mirror lock up on the moon is just absolutely nothing in focus I will post photos later when home.
Thanks
 
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Well Danski0224 i think you were correct i went out this afternoon and left the windows open in the truck so the lens was cold when i got out of the truck with my dog and man i am in love thanks very much below are a couple photos of my 1yr old 145pnd St.Bernard.
 

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