I've seen other people post with what looked to be similar problems, and I think I've found a fix, so…
On my site (www.jell-o.net), I have wordpress installed in a separate directory ("/wordpress"), but set up to appear without needing the "/wordpress/" directory in the path. (See http://codex.wordpress.org/Giving_WordPress_Its_Own_Directory for more info).
Everything was working fine in Firefox, but for Internet Explorer, I was getting "Page Not Found" errors with the Photon photo gallery. I realized that the problem was that photon was still appending "/wordpress/" into the path's that it was creating. When I manually removed the extra directory in the path, IE worked fine.
I think the problem is/was in the definition of PHOTON_ROOT_PATH in photon.php. I changed it from using get_bloginfo('wpurl') to get_bloginfo('url') and now all seems to be fine. I don't know if I broke anything else, but haven't noticed anything yet.
Hopefully this doesn't break anything and other people can find it useful.