Hopefully the following helps someone...
There's a solution in another thread for the Google Analyticator plugin, but the Google Analytics plugin (Boakes v0.68) also has a similar problem with Wordpress 2.7 - ie homepage links in comments have: "'%20rel='external%20nofollow" appended to the end of the URL.
To fix it, the following should work. Find the code:
function comment_author_link($text) {
static $anchorPattern = '(.*href\s*=\s*)[\"\']*(.*)[\"\'] (.*)';
and replace it with:
function comment_author_link($text) {
static $anchorPattern = '(.*href\s*=\s*)[\"\']*(.*\?)[\"\'] (.*)';