I've been having problems with the Module giving incorrect links (back to the home page rather than article) when listing most commented. I'm using sh404sef and tried all the fixes mentioned on the board without luck.
I then got digging in the code and found there is an error in line 80 of mod_comments.class.php
It should read
$id = $row['contentid'];
not
$id = $row['id'];
I hope this helps.