Just wanted to update that I have searched in Joomla forum - both in extensions/components and JA Purity template, and also in Google under several permutations of the subject line of this post.
The only idea that came up along the way was setting the configuration.php variables for log, temp, and live site to absolute paths. So, I tried that and uninstalled/reinstalled. Still no change, except one image in my header moved, when viewed in Mozilla. (Not in IE6). Haven't been able to undo that by restoring configuration.php variables to what they were before, so I'm honestly not sure if there is some type of conflict with Phoca Gallery that is causing the header issue, because I've only been making changes related to this component.
I tried abandoning component and using plug-in in an article -followed instructions & FAQ - that didn't work at all.
Also - spent a few hours pouring through library files and js files in the template, in the Phoca Gallery component, and in Joomla install (I'm on 1.5.6), and could not confidently recognize a command related to the the relationship between the modal box and the site url.
Someone else is having an issue with the JA Purity template and the modal box, so I cross-posted here
http://forum.joomla.org/viewtopic.php?f=541&t=319645, with a link to this post in case the issues are related. Hopefully that did not violate forum ettiquite, if so, I sincerely apologize. I'm trying very hard to explore all the options and come up with a solution.
What continues to perplex me is that the Gallery & modal box worked with the JA Purity template at one point. I don't have solid evidence that the break is directly linked to moving the site out of the root. Is it at all possible that the security patch 1.5.6 caused the issue, as I checked that code and there are some lines concerning pop-up views?
Sorry for the long posts, but I'm trying to share all the appropriate information. Being that the JA Purity template is a standard template with Joomla, and the Phoca Gallery component seems to be so widely used, it would seem to benefit many if a solution could be determined. Any advice would be greatly appreciated.