This lens is known to be "not that great" when it is wide-open at f/6.3. Additionally, I agree with Didereaux's comments above--shot 1 looks like it has some motion blurring, but #2 has less--look at the white cap on the flag shaft, see the ghost outline. The camera settings of ISO 125, 550mm, and 1/800 second are really not very good settings. First off, every single report from every user has stated that this lens is **not** that good at the long end at f/6.3...it's just...not. Your ISO level is too low because it left you at 1/800 second with a 550mm focal length, and multiplied by 550mm is 841.5mm...the 1/over focal length guideline is not quite met....but the real world guideline I go by is TWICE the effective focal length on lens lengths over 200mm...plus, additionally, that flag is whipping in the wind. SHot 1 looks to me like motion blurring, but also, combined with that thin layer of veiling glare over the image...that subtle, gentle hazy look called veiling glare (that term must be 100 years old).
Luckily, you were photographing indoors, thus sheltered from the wind, but the flag is whipping hard, and it appears to me to be recorded with a slight bit of wind-motion blurring. And I can see the image lacks a bit of contrast, due to the veiling. In this testing scenario there's only ONE, single plane of focus that the lens can resolve and show sharpness at, and that plane is the thickness of the flag fabric. To evaluate a front- or back focus issue, you would need a subject that has more than air, located in the immediate area of the focused distance; something like the side of a large, brick building, shot at an angle, would make a good target that would allow you to check focus.
I looked at 1 and 2--I think your focus is pretty close to dead-on: LOOK at the stitching thread--it is resolved fairly clearly as a line of stitching, but the lens is not pro-grade at f/6.3, it shows low contrast, and low resolving ability, and 1/800 in a stiff breeze is just not a good shutter speed on what is, likely, an oscillating flag. From the tests I've seen, and the actual pictures I have seen from your lens, it's NOT "that good" of a lens at the longer end. Long lenses, over 300mm, often show image quality issues caused by uncorrected chromatic aberration; it generally takes ED glass to get rid of that.
I'd look for a non-moving, solid target, and get the shutter speed at least 50% higher, to 1/1250 or so, and try f/8 at the long end: I think that veiling, that hard-to-describe look, will be reduced a good deal. F/8 is 2/3 of a stop down from wide-open, so I expect you'll be a lot happier at f/8 than you are f/6.3. But it WILL MANDATE that you step the ISO level UP from 125 during the winter.