Thanks again for your help, Wiz! After taking your advice and just unzipping the build without doing anything, noticing it working fine, and then suddenly noticing it breaking -- without me doing anything -- I think I've figured out the issue: IETab! For some reason, going back and forth with IETab eventually results in the javascript not working, but things are fine if I restart FF3 again (or preview the page in IE from a separate window). I don't seem to be having this problem with Shadowbox 1.0, though, which is... odd.
So I guess in keeping with this thread, my advice would be for folks to make absolutely sure that IETab isn't mucking something up in the background!
Anyway, now that that issue's been identified, I'm only having one other problem. I've modified the skin and css files so that the titles slide down from the bottom rather than sliding up from the top -- no problems with that; I found the * -1 multiplier and rearranged the div tags so that all seems to be in order. But whereas in v1.0 I used -- height: 100% -- for #shadowbox_title to get the element to fit itself to the captions (sometimes I have rather lengthy ones), that doing that in v2.0 causes the script to not work in IE. Still works fine in FF3, though. Any ideas about that?