General Support: Exact duplicate of copied theme behaves differently from original...

I'm puzzled by this:

I'm using the lightbox theme (1.0). I copied it because I wanted to add the thickbox script instead of the lightbox. This means using a 'class=thickbox' in place of 'rel=lightbox' in album.php and linking to two thickbox .js files and one css file in the head.php and removing those that link to the lightbox script. (I'm already using the thickbox script from within wordpress).

The result was that plogger moved to the right as if the css was broken. I tried all kinds of things like deleting all the links to thickbox but the result was the same.

Then I started a test: I copied the working theme and named it "lightbox two". I changed nothing(!). When I activate this theme the result is the same as above: the plogger part of the page is moved to the right, the same amount of pixels as my sidebar + contentmargin.

I'm really puzzled by this. How can an exact duplicate of a theme behave differently?