From UPGRADING:
. The resultant HTML of highlight_string and highlight_file has changed.
Whitespace between outer HTML tags is removed. Newlines and spaces
are no longer converted to HTML entities. The whole HTML is now wrapped in
<pre> tag. The outer <span> has been merged with <code>.
This has altered the styling of highlighted PHP code (most noticeably the padding around code blocks has been lost) in both the XHTML and Web formats.