Update: Clicking on the archive page links actually results in a 404 “page not found”.
Unless I’m missing something I don’t believe I am.
Here’s the code again, this time showing the variable being set.
$thepage = (get_query_var('paged')) ? get_query_var('paged') : 1;
query_posts('s='.$search_term.'&paged='.$thepage.'&cat='.$cat.',&posts_per_page='.$per);
The exact same code is working for paginating my search results, but in the archive the page links (1,2,3 etc.) come up, but take you back to the home page.
Thanks for your quick reply by the way!