Again, maybe I didn't word it right.
the function get_page_templates() in theme.php in wp-admin/includes is what is called to find all the templates that you have, there is no limit.
However:
function get_page_templates() {
$themes = get_themes();
$theme = get_current_theme();
If will *not* find new theme files if 1) your directory information is cached somehow or 2) your theme is different now then it was when you generated the theme template list previously to you finding it broken.
So I would think switching themes and checking the templates on another theme and switching back would be one solution else if it's still the same I would check what cache'ing you have going on. PHP Speedy would cause this to happen, maybe a few others.