New sites created with New Blog Template only copy some theme settings from WPMU Nelo

I've been using this plugin and so far so good. Just one issue at this point. I've got the template site's theme set to WPMU Nelo. This theme has a customizeable homepage and theme options, exactly the kind of thing I am looking for.

When I create a new site based off the template only some of the settings copy.

Front page text and links - YES!
Front page uploaded images - NO
Theme options - NO (at least not the colors that I've changed so far).

If it all worked or all didn't that would make sense, but half and half doesn't seem right. Any chance that all the data could be copied across? If not where would I start to make this happen. Would it be a customization to this plugin? Where is the 'list' so to speak of things this plugin decides to copy.

Thanks!