I think I got to the root of your problem, the listed IPv6 address is invalid. Is there any chance you have configured IPv6 proxy (either http proxy or socks proxy) in your system? Because it looks like IPv6 address and port (8049).

You can check the environment variable http_proxy if it contains some value by doing:

echo $http_proxy

or check your network settings.

Another place where you could have the proxy defined is in the APT configuration which resides in /etc/apt/apt.conf file or /etc/apt/apt.conf.d/ directory. You should look for Acquire::http::Proxy "<URI>"; setting or written in the block:

Acquire

{

  http

  {

    Proxy "<URI>";

  };

};

Also remember when working with raw IPv6 addresses and URIs to enclose IPv6 address into brackets like this http://[2001:db8:dbb:1:1:1:1:221]:8049/

This might look similar:

# http_proxy=2001:db8:dbb:1:1:1:1:221:8049 apt-get update

Err http://ftp.cz.debian.org wheezy InRelease                             

Err http://security.debian.org wheezy/updates InRelease                   

Err http://ftp.cz.debian.org wheezy Release.gpg

  Could not resolve 'db8:dbb:1:1:1:1:221'

Err http://security.debian.org wheezy/updates Release.gpg

  Could not resolve 'db8:dbb:1:1:1:1:221'

Reading package lists... Done

W: Failed to fetch http://ftp.cz.debian.org/debian/dists/wheezy/InRelease  

W: Failed to fetch http://security.debian.org/dists/wheezy/updates/InRelease  

W: Failed to fetch http://ftp.cz.debian.org/debian/dists/wheezy/Release.gpg  Could not resolve 'db8:dbb:1:1:1:1:221'

W: Failed to fetch http://security.debian.org/dists/wheezy/updates/Release.gpg  Could not resolve 'db8:dbb:1:1:1:1:221'

W: Some index files failed to download. They have been ignored, or old ones used instead.

More general hints:

You can check the IPv6 configuration from the command line using the ip command:

Address:

# ip -6 a s

1: lo: <LOOPBACK,UP,LOWER_UP> mtu 16436 

    inet6 ::1/128 scope host 

       valid_lft forever preferred_lft forever

2: eth0: <BROADCAST,MULTICAST,UP,LOWER_UP> mtu 1500 qlen 1000

    inet6 2a01:5f0:1006::59bb:820d/64 scope global 

       valid_lft forever preferred_lft forever

    inet6 fe80::5054:ff:fe6a:a954/64 scope link 

       valid_lft forever preferred_lft forever

and routes:

# ip -6 r s

2a01:5f0:1006::/64 dev eth0  proto kernel  metric 256 

fe80::/64 dev eth0  proto kernel  metric 256 

default via 2a01:5f0:1006::1 dev eth0  metric 1024 

Anyway since the normal modus of operation is to try the IPv6 address first and then fallback to IPv4, and this is not happening, you also should check your APT configuration for any hosts written as IPv6 address or hosts which do resolve only to IPv6 address (as already suggested by dobey). You might also want to check your /etc/hosts file, where you could have manually written a mapping from .deb archive hostname to IPv6-only address – you can verify this by pinging at the hostname(s) from your APT configuration (check /etc/apt/sources.list file and all files in /etc/apt/sources.list.d/ directory).

Also check your proxy (system or just APT) configuration, because it might creep in unexpected when you have long forgotten about this setting.