Preupgrade F11 -> F12: can't continue after reboot

[dasi]

Preupgrade script completes just fine but upgrading fails after reboot. Grub loads
"Upgrade to Fedora 12 (Constantine)" automatically after reboot (later after failed upgrade this grub entry remains in the list an can be selected manually). Upgrade process starts to load, and just after Graphics interface is loaded it displays small window with "Finding storage devices" and after that the following warning window appears:

<window title>Warning</window title>

Error processing drive:

/dev/sda
305243MB
ATA SAMSUNG HM320JI

This device may need to be reinitialized.

REINITIALIZING WILL CAUSE ALL DATA TO BE LOST!

Device details:
pci-0000:00:1f.2-scsi-0:0:0:0

With the two buttons "Ignore drive" and "Re-initialize drive"

I'm choosing "Ignore drive" of course, because I don't want to loose my data.
Ant after that I'm getting another message window:

<window title>Upgrade root not found</window title>

The root for the previously installed system was not found.

And one button below "Exit installer" - which exits installer process and reboots computer.

Any ideas?

[dasi]

Still trying to resolve this problem by myself. I found recently that partition table on disk of this problematic laptop has overlapping partitions. I think they could appear because of previuos defective HDD which was replaced by warranty, and all the data was copied 1:1 to the new replaced HDD. Here is the output of 'fdisk -lu /dev/sda':

Disk /dev/sda: 320.0 GB, 320072933376 bytes
255 heads, 63 sectors/track, 38913 cylinders, total 625142448 sectors
Units = sectors of 1 * 512 = 512 bytes
Disk identifier: 0x60bbe8ec

   Device Boot      Start         End      Blocks   Id  System
/dev/sda1   *          63    83891429    41945683+   7  HPFS/NTFS
/dev/sda2        83891430   302150519   109129545    7  HPFS/NTFS
/dev/sda3       302150520   616735349   157292415    5  Extended
/dev/sda4       616735350   625137344     4200997+  82  Linux swap / Solaris
/dev/sda5   *   302150583   302568209      208813+  83  Linux
/dev/sda6       302560184   616743325   157091571   83  Linux

And also output of fdisk verify command:

Warning: partition 4 overlaps partition 6.
Warning: partition 5 overlaps partition 6.
Logical partition 6 not entirely in partition 3
5224 unallocated 512-byte sectors

Now the question is how to fix it without losing data. Note that current system is running without any problems yet. I think i will need some fdisk with option to manually entering partition sizes/boundaries by hand. But how to calculate these values? For example i have: "total 625142448 sectors" - so what should be the last sector number in the partition table, look at /dev/sda3 which end is 616735349, so it means that extended partition is already out of the bound, or do i need to add some offset to this value?
Btw: /dev/sda5 is /boot and /dev/sda6 is /