So I ended up just using a different script and things work fine now. I think there was a persist function in the first script that was interfering with the cookies. Thanks for your help though! And again, it’s an excellent plugin that really enhances the function of my site.
I think some javascript that I’m running for the menu on the left is causing the problem. I removed it and I think Smarter Navigation is working properly now.
Have you run into javascript conflicts before with the plugin?
Did anyone ever find a proper solution to this issue? I’ve been killing myself trying to figure it out. W5f3dj7, could you possibly share the alterations you made to the WP core file to implement the rollover?