I've never encountered this problem since working with WP 3.0.1/A 3.5.3. If you go to www.capayorganic.com/indexwp.php (client doesn't want the WordPress index available yet as default), you'll see the dynamic header is aligned left with the second image in the sequence centered beneath it.
I've only used 3.5.3 for a few sites now, so I'm still learning some of the quirks. I never had this happen with 3.4.6, so is there a setting to center this? I have the following settings:
Layout width: 980px
Layout container padding: 5px
Header Image > Alignment: Top Center
If it makes a difference, the image size is 946x224. If I sent the layout width to match the image, then everything's fine.
What's strange is that when it first loads, you'll see the image is centered, then after a second it moves left. I saw a previous thread on something like this but it sounds like the guy didn't upgrade to 3.5.3 and forced a fix on a previous version.
Thoughts? Thanks for your input!