I've got a similar problem.
Dapper Drake 6.06.1 32bit on AMD64

Clicking "Install Updates" with having market all availible updates just show's
"Examing your system" and then doesn't install anything. The updates are still 
available.
Sometimes there are some updates, which can be installed.

Console:

sudo update-manager
Password:
/usr/lib/python2.4/site-packages/apt/__init__.py:17: FutureWarning: apt API not 
stable yet
  warnings.warn("apt API not stable yet", FutureWarning)


apt-get upgrade works with those updates, update-manager rejects to install:

sudo apt-get upgrade
Reading package lists... Done
Building dependency tree... Done
The following packages will be upgraded:
  amarok amarok-engines amarok-xine
3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 14.6MB of archives.
After unpacking 6871kB of additional disk space will be used.
Do you want to continue [Y/n]? Y
Get:1 http://archive.ubuntu.com dapper-backports/main amarok-xine 
2:1.4.2-0ubuntu2~dapper1 [54.6kB]
Get:2 http://archive.ubuntu.com dapper-backports/universe amarok-engines 
2:1.4.2-0ubuntu2~dapper1 [840B]
Get:3 http://archive.ubuntu.com dapper-backports/main amarok 
2:1.4.2-0ubuntu2~dapper1 [14.5MB]
Fetched 14.6MB in 5m13s (46.5kB/s)
(Reading database ... 146603 files and directories currently installed.)
Preparing to replace amarok-xine 2:1.4.1-0kubuntu2 (using 
.../amarok-xine_2%3a1.4.2-0ubuntu2~dapper1_i386.deb) ...
Unpacking replacement amarok-xine ...
Preparing to replace amarok-engines 2:1.4.1-0kubuntu2 (using 
.../amarok-engines_2%3a1.4.2-0ubuntu2~dapper1_i386.deb) ...
Unpacking replacement amarok-engines ...
Preparing to replace amarok 2:1.4.1-0kubuntu2 (using 
.../amarok_2%3a1.4.2-0ubuntu2~dapper1_i386.deb) ...
Unpacking replacement amarok ...
Setting up amarok-xine (1.4.2-0ubuntu2~dapper1) ...
Setting up amarok (1.4.2-0ubuntu2~dapper1) ...

Setting up amarok-engines (1.4.2-0ubuntu2~dapper1) ...

-- 
Update Manager does not install updates
https://launchpad.net/bugs/26677

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