If you could enable your debug log and hit the page with encryption running on 3.0 or later see if you get any errors or warnings. And/or add a small little plugin or in your functions.php, grab your key from your File Away config page and do this:
$key = PUTYOURKEYHERE;
$file = PUTAURLHERE;
$encrypted = urlencode(trim(base64_encode(mcrypt_encrypt(MCRYPT_RIJNDAEL_256, $key, $file, MCRYPT_MODE_ECB, mcrypt_create_iv(mcrypt_get_iv_size(MCRYPT_RIJNDAEL_256, MCRYPT_MODE_ECB), MCRYPT_RAND)))));
$decrypted = urldecode(trim(mcrypt_decrypt(MCRYPT_RIJNDAEL_256, $key, base64_decode($encrypted), MCRYPT_MODE_ECB, mcrypt_create_iv(mcrypt_get_iv_size(MCRYPT_RIJNDAEL_256, MCRYPT_MODE_ECB), MCRYPT_RAND))));
echo $encrypted.'<br>'.$decrypted;
See if you get any errors.