Did you set up the url rewrite in your webserver? I have also Raspbian, but I use lighthttp for webserver. I had to set up these /etc/lighttpd/lighttpd.conf to get work the download urls properly eg. for my Kobo reader. Maybe it helps you:
server.modules += ("mod_rewrite")
server.document-root = "/media/hdd/www"
url.rewrite-once = ("/cops/download/(.*)/.*\.(.*)$" => "/cops/fetch.php?data=$1&type=$2",
"^/cops/download/(\d+)/(\d+)/.*\.(.*)$" => "/cops/fetch.php?data=$1&db=$2&type=$3")
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