The conditions needed to reproduce the bug are:
- a source file which would have some text rendered in italic. I used a C file with many comments in it
- a windows web browser. I used Chrome 21
The annotated source view will show the line numbers and annotations starting some distance below the top of their box. Closer investigation will show that all columns have the same number of lines in them, but all line numbers and annotations are 15px high, while all bits of source code that are in italics are 16px high, ruining the whole layout.
This is a combination of the unfortunate windows font rendering behavior, where asking for italics makes your text one pixel higher, and some misplaced CSS. Some well-meaning person has placed line-height: 15px on div.code-highlight, but setting line-height on a block element containing inline elements (like the spans wrapping all text) only defines a minimum line height for the text contained within them.
In order to set the line height to a fixed value, either set line-height on the inline span elements themselves, or make the spans inline-block elements. I think.