I am using Ver 3.5.3.
I have 2 header images 1300/160 pix size. When I enter anything but 0 in "New fade in/out header image" it moves the header image to the right. The image still fills the compete header area. Does not matter what the alignment is set too presently at "Top Center". Otherwise everything seems to work fine. I cannot leave a URL as I am experimenting with different header ideas on my local host using wamp.
Any suggestion.

Bob

Not a fix, but after some experimenting I found if reduced the header size to 960 x 160 The image did not move when I selected "new fade in/out"

Thanks all, Bob

this is a known issue with the fade in/out - it doesn't pay attention to the position of the header image along with overlaying the blog title (if you have it set to display over the header)

Do not get use to it, it will most likely be removed in 3.6.5

Strange it worked fine in localhost when I shortened the image but when I uploaded to my site the image became a tads smaller, and although all the 3 images were the same size they became offset. Take a look at http://2bretired.com

Thanks, Bob

OK
Today I played around with image size and found a compromise size that did not shift, but only looked at it on Firefox and IE8.

I hope you keep this function in any future updates with maybe a disclaimer of the known problem.

Thanks, Bob