Similar happened to me upon update manager upgrade to grub -pc 1.99-21ubuntu3.4. The "COnfigure Grub Devices" dialog offered choices of /dev/sda and /dev/sda6. Selecting both of these, the Details display of update manager showed 

/usr/sbin/grub-probe: error: cannot stat '/,'

I deselected /dev/sda6 and continued. Afterwards, but not rebooting yet, I see the following. This (as can be seen) is a dual-boot Win7 / Ubuntu 12.04 machine. 

[code]
~$ fdisk -l

Disk /dev/sda: 250.1 GB, 250059350016 bytes
255 heads, 63 sectors/track, 30401 cylinders, total 488397168 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0x29133921

   Device Boot      Start         End      Blocks   Id  System
/dev/sda1   *        2048   209717247   104857600    7  HPFS/NTFS/exFAT
/dev/sda2       209717248   241174527    15728640   1b  Hidden W95 FAT32
/dev/sda3       241176574   488355839   123589633    5  Extended
/dev/sda4       488355840   488397167       20664   ef  EFI (FAT-12/16/32)
/dev/sda5       480356352   488355839     3999744   82  Linux swap / Solaris
/dev/sda6       241176576   476184575   117504000   83  Linux
/dev/sda7       476186624   480344063     2078720   82  Linux swap / Solaris

Partition table entries are not in disk order

Disk /dev/mapper/cryptswap1: 2128 MB, 2128609280 bytes
255 heads, 63 sectors/track, 258 cylinders, total 4157440 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0x26f89c28

Disk /dev/mapper/cryptswap1 doesn't contain a valid partition table
[/code]

(The /dev/sda7 second swap was created by the upgrade process from 11.10 to 12.04)

Then I ran:
[code]
~$ update-grub
Generating grub.cfg ...
Found linux image: /boot/vmlinuz-3.2.0-31-generic-pae
Found initrd image: /boot/initrd.img-3.2.0-31-generic-pae
Found linux image: /boot/vmlinuz-3.2.0-30-generic-pae
Found initrd image: /boot/initrd.img-3.2.0-30-generic-pae
Found linux image: /boot/vmlinuz-3.2.0-29-generic-pae
Found initrd image: /boot/initrd.img-3.2.0-29-generic-pae
Found memtest86+ image: /boot/memtest86+.bin
Found Windows 7 (loader) on /dev/sda1
Found Windows Recovery Environment (loader) on /dev/sda2
done
[/code]

and found

[code]
~$ debconf-show grub-pc
  grub-pc/kopt_extracted: false
  grub2/kfreebsd_cmdline:
  grub2/device_map_regenerated:
* grub-pc/install_devices:
  grub-pc/postrm_purge_boot_grub: false
  grub-pc/install_devices_failed_upgrade: true
  grub-pc/disk_description:
* grub2/linux_cmdline:
* grub-pc/install_devices_empty: true
  grub2/kfreebsd_cmdline_default: quiet
  grub-pc/partition_description:
  grub-pc/install_devices_failed: false
* grub-pc/install_devices_disks_changed:
* grub2/linux_cmdline_default: quiet splash
  grub-pc/chainload_from_menu.lst: true
  grub-pc/hidden_timeout: false
  grub-pc/mixed_legacy_and_grub2: true
  grub-pc/timeout: 10
[/code]

As stated above, dpkg-reconfigure was successful from the cmd line:

[code]
~$ dpkg-reconfigure --frontend=gnome grub-pc
Generating grub.cfg ...
Found linux image: /boot/vmlinuz-3.2.0-31-generic-pae
Found initrd image: /boot/initrd.img-3.2.0-31-generic-pae
Found linux image: /boot/vmlinuz-3.2.0-30-generic-pae
Found initrd image: /boot/initrd.img-3.2.0-30-generic-pae
Found linux image: /boot/vmlinuz-3.2.0-29-generic-pae
Found initrd image: /boot/initrd.img-3.2.0-29-generic-pae
Found memtest86+ image: /boot/memtest86+.bin
Found Windows 7 (loader) on /dev/sda1
Found Windows Recovery Environment (loader) on /dev/sda2
done
[/code]

(I am posting this now and will comment again in a while after I back up the drive before rebooting)