That happens a lot… technically it should be that plugins work with themes rather than the other way around, unless a theme is built around a specific plugin. What is it that this plugin is supposed to do that is not working in the theme? You mentioned it appends to the blog, but what gets appended?
Perhaps I can take a quick look but I cannot guarantee anything because this is related to a third party product.
NOTE: Does this work with any of the default WordPress themes?