I think the actual problem is with the way the java script interacts with the blocks. Normally under topics there are blocks on the right side of an article. Your script is telling it to put different blocks then the normal ones in one of your themes.

Normally when you decide to load a block you tell nuke to put it on the left or right or center through the admin cp. I don't believe you are doing that with yours because you have it set opposite for your seperate themes. So basically you tell the block go here, but the script tells it to go somewhere else. That is creating a conflict, basically confusing your server.

If you changed it and made it so that the blocks showed up on the same side for both themes and were set through admin cp, I bet the problem goes away.

You might want to check your html to see if any errors have been inserted there (sometimes happens instead of displaying the error), or try turning debugging on. It wouldn't suprise me if something shows up that was previously hidden.