Eu tive o mesmo problema que você:
$ sudo apt-get --reinstall install intel-microcode
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following package was automatically installed and is no longer required:
linux-image-686-pae
Use 'apt-get autoremove' to remove it.
0 upgraded, 0 newly installed, 1 reinstalled, 0 to remove and 14 not upgraded.
Need to get 426 kB of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 http://ftp.de.debian.org/debian/ sid/non-free intel-microcode i386 1.20130222.5 [426 kB]
Fetched 426 kB in 11s (36.8 kB/s)
(Reading database ... 283637 files and directories currently installed.)
Preparing to replace intel-microcode 1.20130222.5 (using .../intel-microcode_1.20130222.5_i386.deb) ...
Unpacking replacement intel-microcode ...
Setting up intel-microcode (1.20130222.5) ...
Updating microcode on all online processors...
update-initramfs: deferring update (trigger activated)
Processing triggers for initramfs-tools ...
update-initramfs: Generating /boot/initrd.img-3.9-1-686-pae
Error: Timeout was reached
$
Em seguida, estava pensando que initramfs tem algo a ver com isso, com uma dica que recebi do arquivo dpkg.log .
2013-07-13 13:54:57 startup archives unpack 2013-07-13 13:55:09 upgrade intel-microcode:i386 1.20130222.5 1.20130222.5 2013-07-13 13:55:09 status half-configured intel-microcode:i386 1.20130222.5 2013-07-13 13:55:09 status unpacked intel-microcode:i386 1.20130222.5 2013-07-13 13:55:09 status half-installed intel-microcode:i386 1.20130222.5 2013-07-13 13:55:10 status half-installed intel-microcode:i386 1.20130222.5 2013-07-13 13:55:10 status unpacked intel-microcode:i386 1.20130222.5 2013-07-13 13:55:10 status unpacked intel-microcode:i386 1.20130222.5 2013-07-13 13:55:11 startup packages configure 2013-07-13 13:55:11 configure intel-microcode:i386 1.20130222.5 2013-07-13 13:55:11 status unpacked intel-microcode:i386 1.20130222.5 2013-07-13 13:55:11 status unpacked intel-microcode:i386 1.20130222.5 2013-07-13 13:55:11 status unpacked intel-microcode:i386 1.20130222.5 2013-07-13 13:55:12 status half-configured intel-microcode:i386 1.20130222.5 2013-07-13 13:55:12 status installed intel-microcode:i386 1.20130222.5 2013-07-13 13:55:12 status triggers-pending initramfs-tools:all 0.113 2013-07-13 13:55:12 trigproc initramfs-tools:all 0.113 2013-07-13 13:55:12 status half-configured initramfs-tools:all 0.113 2013-07-13 13:55:44 status installed initramfs-tools:all 0.113
Por isso, continuo a reinstalar o pacote initramfs-tools usando apt-get --reinstall install initramfs-tools e agora a mensagem ficou em silêncio.
$ sudo apt-get --reinstall install intel-microcode
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following package was automatically installed and is no longer required:
linux-image-686-pae
Use 'apt-get autoremove' to remove it.
0 upgraded, 0 newly installed, 1 reinstalled, 0 to remove and 14 not upgraded.
Need to get 0 B/426 kB of archives.
After this operation, 0 B of additional disk space will be used.
(Reading database ... 283637 files and directories currently installed.)
Preparing to replace intel-microcode 1.20130222.5 (using .../intel-microcode_1.20130222.5_i386.deb) ...
Unpacking replacement intel-microcode ...
Setting up intel-microcode (1.20130222.5) ...
Updating microcode on all online processors...
update-initramfs: deferring update (trigger activated)
Processing triggers for initramfs-tools ...
update-initramfs: Generating /boot/initrd.img-3.9-1-686-pae
$
Eu não sei as razões exatas para isso (nem como reproduzi-lo) e o google não ajuda nesse assunto, mas deixei aqui uma possível solução. Mas se eu tivesse que fazer uma suposição, talvez o tempo limite fosse devido aos gatilhos que expiraram já que, para ambos, isso aconteceu depois que alguns gatilhos foram usados ( menu no caso de OP, update-initramfs no meu).