Well, post #2 is from yesterday. Today I've tried reinstalling, and this
is what I did:

•Download from US mirror. OK
•Check integrity with MD5 hash. OK
•Created an USB Startup Disk. OK
•Reinstalled Ubuntu from USB. I have partitions for /, swap, and /home. I 
format /dev/sda1 as ext4 for /. Others not modified.
•Boot into new Ubuntu. OK
•Login as ilhuitemoc. I have several startup programs, but as they are not 
installed, they can't start.
•Run the following commands to add repos:
sudo add-apt-repository ppa:webkit/ppa
sudo add-apt-repository ppa:midori/ppa
sudo add-apt-repository ppa:pidgin-developers/ppa
sudo add-apt-repository ppa:banshee-team/ppa
sudo add-apt-repository ppa:dockbar-main/ppa
sudo add-apt-repository ppa:compiz/ppa
sudo add-apt-repository ppa:gnomenu-team/ppa
sudo add-apt-repository ppa:cairo-dock-team/ppa
sudo add-apt-repository ppa:do-core/ppa
sudo add-apt-repository ppa:gm-notify-maintainers/ppa
sudo wget --output-document=/etc/apt/sources.list.d/medibuntu.list 
http://www.medibuntu.org/sources.list.d/$(lsb_release -cs).list && sudo apt-get 
--quiet update && sudo apt-get --yes --quiet --allow-unauthenticated install 
medibuntu-keyring && sudo apt-get --quiet update
•Install the packages found in the attachment (which were in a functional 
Ubuntu install before)
•Wait for download and install. OK
•To be sure there's nothing wrong, I updated the repos. No errors.
•I install prism-google-mail (could have been another app; doesn't matter)
sudo apt-get install prism-google-mail
•I test it, and decide I don't like it, so I proceed to remove
$ sudo apt-get remove prism-google-mail
[   47.533432] ata3.00: exception Emask 0x0 SAct 0x1 SErr 0x0 action 0x0
[   47.533486] ata3.00: irq_stat 0x40000008
[   47.533520] ata3.00: failed command: READ FPDMA QUEUED
[   47.533563] ata3.00: cmd 60/a0:00:90:78:2d/00:00:00:00:00/40 tag 0 ncq 81920 
in
[   47.533565]          res 41/40:00:1f:79:2d/a2:00:00:00:00/40 Emask 0x409 
(media error) <F>
[   47.533667] ata3.00: status: { DRDY ERR }
[   47.533695] ata3.00: error: { UNC }
[   47.560912] ata3.00: configured for UDMA/133
[   47.560922] ata3: EH complete
[   50.475187] ata3.00: exception Emask 0x0 SAct 0x1 SErr 0x0 action 0x0
[   50.475236] ata3.00: irq_stat 0x40000008
[   50.475269] ata3.00: failed command: READ FPDMA QUEUED
[   50.475312] ata3.00: cmd 60/a0:00:90:78:2d/00:00:00:00:00/40 tag 0 ncq 81920 
in
[   50.475314]          res 41/40:00:1f:79:2d/a2:00:00:00:00/40 Emask 0x409 
(media error) <F>
[   50.475416] ata3.00: status: { DRDY ERR }
[   50.475444] ata3.00: error: { UNC }
[   50.504738] ata3.00: configured for UDMA/133
[   50.504747] ata3: EH complete
[   53.418992] ata3.00: exception Emask 0x0 SAct 0x1 SErr 0x0 action 0x0
[   53.419038] ata3.00: irq_stat 0x40000008
[   53.419070] ata3.00: failed command: READ FPDMA QUEUED
[   53.419113] ata3.00: cmd 60/a0:00:90:78:2d/00:00:00:00:00/40 tag 0 ncq 81920 
in
[   53.419115]          res 41/40:00:1f:79:2d/a2:00:00:00:00/40 Emask 0x409 
(media error) <F>
[   53.419216] ata3.00: status: { DRDY ERR }
[   53.419244] ata3.00: error: { UNC }
[   53.448555] ata3.00: configured for UDMA/133
[   53.448562] ata3: EH complete
[   56.362816] ata3.00: exception Emask 0x0 SAct 0x1 SErr 0x0 action 0x0
[   56.362864] ata3.00: irq_stat 0x40000008
[   56.362897] ata3.00: failed command: READ FPDMA QUEUED
[   56.362941] ata3.00: cmd 60/a0:00:90:78:2d/00:00:00:00:00/40 tag 0 ncq 81920 
in
[   56.362943]          res 41/40:00:1f:79:2d/a2:00:00:00:00/40 Emask 0x409 
(media error) <F>
[   56.363043] ata3.00: status: { DRDY ERR }
[   56.363071] ata3.00: error: { UNC }
[   56.392366] ata3.00: configured for UDMA/133
[   56.392375] ata3: EH complete
[   59.462159] ata3.00: exception Emask 0x0 SAct 0x1 SErr 0x0 action 0x0
[   59.463951] ata3.00: irq_stat 0x40000008
[   59.465779] ata3.00: failed command: READ FPDMA QUEUED
[   59.467562] ata3.00: cmd 60/a0:00:90:78:2d/00:00:00:00:00/40 tag 0 ncq 81920 
in
[   59.467563]          res 41/40:00:1f:79:2d/a2:00:00:00:00/40 Emask 0x409 
(media error) <F>
[   59.471246] ata3.00: status: { DRDY ERR }
[   59.473075] ata3.00: error: { UNC }
[   59.502824] ata3.00: configured for UDMA/133
[   59.502830] ata3: EH complete
[   62.417084] ata3.00: exception Emask 0x0 SAct 0x1 SErr 0x0 action 0x0
[   62.418903] ata3.00: irq_stat 0x40000008
[   62.420726] ata3.00: failed command: READ FPDMA QUEUED
[   62.422532] ata3.00: cmd 60/a0:00:90:78:2d/00:00:00:00:00/40 tag 0 ncq 81920 
in
[   62.422533]          res 41/40:00:1f:79:2d/a2:00:00:00:00/40 Emask 0x409 
(media error) <F>
[   62.426249] ata3.00: status: { DRDY ERR }
[   62.428114] ata3.00: error: { UNC }
[   62.457717] ata3.00: configured for UDMA/133
[   62.457727] sd 3:0:0:0: [sda] Unhandled sense code
[   62.457730] sd 3:0:0:0: [sda] Result: hostbyte=DID_OK driverbyte=DRIVER_SENSE
[   62.457733] sd 3:0:0:0: [sda] Sense Key : Medium Error [current] [descriptor]
[   62.457738] Descriptor sense data with sense descriptors (in hex):
[   62.457740]         72 03 11 04 00 00 00 0c 00 0a 80 00 00 00 00 00 
[   62.457748]         00 2d 79 1f 
[   62.457751] sd 3:0:0:0: [sda] Add. Sense: Unrecovered read error - auto 
reallocate failed
[   62.457757] sd 3:0:0:0: [sda] CDB: Read(10): 28 00 00 2d 78 90 00 00 a0 00
[   62.457765] end_request: I/O error, dev sda, sector 2980127
[   62.459654] ata3: EH complete
[   65.660838] ata3.00: exception Emask 0x0 SAct 0x6 SErr 0x0 action 0x0
[   65.662747] ata3.00: irq_stat 0x40000008
[   65.664651] ata3.00: failed command: READ FPDMA QUEUED
[   65.666540] ata3.00: cmd 60/00:10:10:60:2d/01:00:00:00:00/40 tag 2 ncq 
131072 in
[   65.666541]          res 41/40:00:a5:60:2d/a2:00:00:00:00/40 Emask 0x409 
(media error) <F>
[   65.670391] ata3.00: status: { DRDY ERR }
[   65.672324] ata3.00: error: { UNC }
[   65.701506] ata3.00: configured for UDMA/133
[   65.701513] ata3: EH complete
[   68.615772] ata3.00: exception Emask 0x0 SAct 0x3 SErr 0x0 action 0x0
[   68.617727] ata3.00: irq_stat 0x40000008
[   68.619651] ata3.00: failed command: READ FPDMA QUEUED
[   68.621568] ata3.00: cmd 60/00:00:10:60:2d/01:00:00:00:00/40 tag 0 ncq 
131072 in
[   68.621570]          res 41/40:00:a5:60:2d/a2:00:00:00:00/40 Emask 0x409 
(media error) <F>
[   68.625411] ata3.00: status: { DRDY ERR }
[   68.627354] ata3.00: error: { UNC }
[   68.667552] ata3.00: configured for UDMA/133
[   68.667562] ata3: EH complete
[   71.581804] ata3.00: exception Emask 0x0 SAct 0x3 SErr 0x0 action 0x0
[   71.583751] ata3.00: irq_stat 0x40000008
[   71.585687] ata3.00: failed command: READ FPDMA QUEUED
[   71.587596] ata3.00: cmd 60/00:08:10:60:2d/01:00:00:00:00/40 tag 1 ncq 
131072 in
[   71.587597]          res 41/40:00:a5:60:2d/a2:00:00:00:00/40 Emask 0x409 
(media error) <F>
[   71.591476] ata3.00: status: { DRDY ERR }
[   71.593408] ata3.00: error: { UNC }
[   71.633584] ata3.00: configured for UDMA/133
[   71.633592] ata3: EH complete
[   74.547845] ata3.00: exception Emask 0x0 SAct 0x3 SErr 0x0 action 0x0
[   74.549809] ata3.00: irq_stat 0x40000008
[   74.551755] ata3.00: failed command: READ FPDMA QUEUED
[   74.553696] ata3.00: cmd 60/00:00:10:60:2d/01:00:00:00:00/40 tag 0 ncq 
131072 in
[   74.553698]          res 41/40:00:a5:60:2d/a2:00:00:00:00/40 Emask 0x409 
(media error) <F>
[   74.557572] ata3.00: status: { DRDY ERR }
[   74.559526] ata3.00: error: { UNC }
[   74.599622] ata3.00: configured for UDMA/133
[   74.599632] ata3: EH complete
[   77.824908] ata3.00: exception Emask 0x0 SAct 0x3 SErr 0x0 action 0x0
[   77.826876] ata3.00: irq_stat 0x40000008
[   77.828848] ata3.00: failed command: READ FPDMA QUEUED
[   77.830769] ata3.00: cmd 60/00:08:10:60:2d/01:00:00:00:00/40 tag 1 ncq 
131072 in
[   77.830771]          res 41/40:00:a5:60:2d/a2:00:00:00:00/40 Emask 0x409 
(media error) <F>
[   77.834770] ata3.00: status: { DRDY ERR }
[   77.836714] ata3.00: error: { UNC }
[   77.876763] ata3.00: configured for UDMA/133
[   77.876770] ata3: EH complete

I've fixed the other errors: Pidgin works, as well as Gnome-Do and
Banshee. But I can't use apt or synaptic anymore.

** Attachment added: "installedsoftware"
   http://launchpadlibrarian.net/48628189/installedsoftware

-- 
Upgrading damages filesystem
https://bugs.launchpad.net/bugs/581514
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