If you ever get in touch with such an error while updating with apt-get / synaptic or manually updating the initram disk via update-initramfs you must have improperly removed a customized kernel version.

update-initramfs: Generating /boot/initrd.img-2.6.nn.nn-nn
Cannot find /lib/modules/2.6.nn.nn-nn
update-initramfs: failed for /boot/initrd.img-2.6.nn.nn-nn

In order to fix this issue you should simply delete the corresponding missing (and removed) kernel file from /var/lib/initramfs-tools