When you have a PRE tag in your HTML, it's supposed to be rendered exactly as written, honoring spacing and such. However, when Concordion.NET processes it, it adds indenting to the first line of it. In fact, the only way to defeat this is to insert a non-breaking space and line-break.

Here's what the HTML file looks like before processing:

Here's what the HTML file looks like after processing:

Here's the HTML file to repro this. The system doesn't like HTML files, so it's zipped.
PreHandlingBug.zip