I am having exactly the same issue.
My tag for getting the links was
<?php get_links('-1', '<li>', '</li>', '', FALSE, 'id', TRUE, TRUE, -1, TRUE); ?>
I changed it to
<?php get_links('-1', '<li>', '</li>', '', FALSE, 'id', TRUE, TRUE, -1, TRUE, TRUE); ?> as MichaelH suggested and nothing changed.
I guess we should use the wp_list_bookmarks tag now. I remember it used to give a lot of troubles in 2.1 (not listing sub-categories and so on), but it must be the tag to use for displaying links in version 2.2.
I really think that it would be better for everyone to launch a list with "things you should change now" with every new release: since I have upgraded to 2.2 I had to change quite a lot of files because of weird errors, the .htaccess file being the most annoying and important thing.