Can you provide a link to an example of what's happening? A screenshot won't tell me anything. I need to be able to inspect the code with
Firebug before I can even begin to see what might be causing the issue.
The framework is fully compatible with all default WordPress processes, which means the theme is as well. If there is any compatibility issue, it is most likely an issue with the plugin, not with the theme or the framework. When having trouble with a plugin, it is always best to check the support for that plugin to see if anyone else is having the same thing happen to them.
It's very possible that the plugin developer is using some javascript or jQuery code that isn't in "noconflict" mode, but as I said, I can't even check that if I can't see the plugin active on your site somewhere.