Yeah, it's pretty strange. Basically, when I activate the plugin/script, and refresh the page (any page in which the comments script is included), the page loads as expected and you can see the current theme has loaded without issue, but once the onload script kicks in, it appears to load the stylesheet from my previous theme, which overrides much of the current theme (in commonly used divs like #header, #footer, #content, h1.title, etc).
I deleted this site from my IntenseDebate account, and re-installed, but that didn't help. I think they just re-activated the old key, so if that was the source of the issue, it remains so.
For reference, I have a couple plugins installed on items/show: Geolocation, Social Bookmarking, and MyOmeka, as well as a jQuery image viewer script called FancyBox.
In any case, I just switched to Disqus, which achieves the same end and works more or less the same.