Looks like a minor glitch here that needs a tweak.
class-theme-my-login-admin.php Code Line 152
Issue: flush_rewrite_rules is triggered when clicking on Settings >>> Theme My Login, which flushes the root .htaccess file. I think the only time this is supposed to be used (according to the WP folks) is on plugin activation and deactivation. Thanks
// Flush rewrite rules if slugs have been updated if ( $theme_my_login->options->get_option( 'flush_rules' ) ) flush_rewrite_rules();