Comment # 2 on bug 987551 from Christian Boltz

I'd guess it's unlikely that AppArmor is causing this bug (even if in theory
extensive logging to audit.log could slow down other IO ;-) - but nevertheless
please check if dmesg or /var/log/audit/audit.log contains large amounts of
AppArmor messsages (or other useful hints).

That still doesn't explain why you also see this with AppArmor disabled.

If I had to guess, I'd say
- double-check your disk - I had cases where a disk was terribly slow without
  showing any errors, and that was a month or two before it died
- try to do only reads or only writes (with dd of=/dev/null or dd if=/dev/zero)
  to find out if reading or writing is the problem (clear the cache or reboot
  to avoid false results by cached files)
- in general, if this is not caused by half-dead hardware, it probably
  qualifies as a kernel bug