There are a few possibilities here. First, your statsme log may have gotten too large, and it takes the statsme plugin a very long time to load it; I recommend you try shutting down your server, then deleting addons/statsme/statsme.log. Second, you may have other admin mod or metamod plugins that cause the mapchanges to be slow (the AMX plugin "csstats" is well-known to cause this, for instance); try disabling plugins to see if that will help. Third, your map files may have lost the hardlink to their source files on the server; you can ask us to run our repair script in this case.
Try deleting the .lst files in the downloadlist directory of your FTP. Disable any custom plugins for basic troubleshooting testing to see if the problem persists.