Pagination doesn't work on homepage : gives 404 error

I am using drupal 6 with CleanPager.
Everything works as its supposed to on various content type pagination pagers.
But the links on the homepage, like: example.com/node/1 gives a 404 error.

I managed to fix it by adding the following line to my .htaccess file:
RewriteRule ^(.*)/(\d+)$ $1&page=$2

Which, i don't quite understand why it works. But it does. After adding the above rule all pagination works correctly.
I suspect this problem my have something to do with the pathauto module installed. And perhaps appending the query with an & rather than a ?