theme_pager() is quite handy, but it will also append alot of form information that you may not need into the page links.
To remove the fields from the URL, prior to your theme_pager() call, unset the variables from $_REQUEST.
// Remove search-button from the pager args
if (isset($_REQUEST['search-button'])) {
unset($_REQUEST['search-button']);
} After that, they should no longer appear in your pager.
