Is there anyway to prevent formatting code in SOURCE mode?

Those markers are HTML comments and they are automatically protected before processing the rest of the protections, so they don't exist when your regexp is run.

The only way to retain your source formatting is to not use a WYSIWYG editor. Use only a textarea because as soon as the browser parses your HTML there's no warranty that any whitespace will remain.

You can search the forums for other posts explaining some of the issues.