Hi... im really desperate for help cuz this deals with important data to be recovered!
Here's the description:

(PS: The post was made a long one so that i could give maximum information for the troubleshooters. Pls. do not avoid helping me for the length of it!)

Two days ago the power went off multiple times when the PC was on and i was forced to fast shutdown it (by holding the power button down continously). The next day when i booted up my pc.., the following error showed up:

"Windows could not start because the following file is missing or corrupt C:\windows\system32\config\system"

I tried to rectify it using instructions at the following link but decided to drop it down at part2 since system restore never works in my PC.
How to recover from a corrupted registry that prevents Windows XP from starting

Finally decided to format my C: drive after transferring some important files from C:\ to the the other partitions of this failed drive. This, i tried to do by connecting the HDD of my dad's computer as a secondary master drive and booting my PC from it.

The failed drive is seagate 250GB SATA drive with following partitions: (im giving the labellings of each partition for easy identification further down when both the HDD's would be connected)

All the partitions are NTFS
Partition 1: 43.95 GB Label- Windows
Partition 2: 43.95 GB Label- Common
Partition 3: 47.85 GB Label- Music
Partition 4: 48.34 GB Label- Freeware
Partition 5: 48.79 GB Label- Backups

My dad's drive (40GB) has partitions as follows:
All the partitions are FAT32
Partition 1: 9.32 GB Label- WindowsXP
Partition 2: 9.32 GB Label- Personal
Partition 3: 9.32 GB Label- Extras
Partition 4: 9.32 GB Label- Common

So, as stated earlier i managed to connect both the HDD on my PC's, boot from my dad's windowsXP and fortunately all my 5 NTFS partitions were visible!
(Refer image: Imageshack - mycomputerbothhdds) The drives G,H,I,J,K labelled with blue font are the NTFS partitions on my SATA HDD)
Hence backed up all the dats on my C: drive to other partitions within my drive and the other HDD as well...

Now ready to format the C: drive and make a fresh installation of WindowsXP onto it.. Disconnected the 40GB FAT32 HDD and installed WindowsXP onto my NTFS HDD's C:\ drive with a bootable WindowsXP CD-ROM... Now, begins the problem!

When all was fine and i booted my fresh installation of XP, to my surprise only 3 partitions out of the 5 were visible!!?
(Refer image: Imageshack - mycomputersatahddalone)

The following partitions were not to be seen...
Partition 4: 48.34 GB Label- Freeware
Partition 5: 48.79 GB Label- Backups
Thats 100GB of data missing!

Worried, i tried connecting the FAT32 HDD again as a secondary master to my PC with the SATA HDD and made it to boot from the FAT32 HDD...
A relief! I could find all the 5 NTFS partitions listed here just perfectly with all the data intact...

The question: Why are the two partitions not being displayed when i boot from the 250GB SATA NTFS drive?
When i go to Start-->My Computer..>Right-click--->Manage--->Disk management under storage, i see the following:

Condition 1. When booting from FAT32 HDD as IDE secondary master with SATA HDD attached:
All the 5 partitions of the SATA HDD are displayed perfectly...
(Refer image: Imageshack - diskmgmtbothhdds)

Condition 2. FAT32 HDD is detached.. Boot from SATA HDD alone..
Only the first 3 partitions as below as shown!

Partition 1: 43.95 GB Label- Windows
Partition 2: 43.95 GB Label- Common
Partition 3: 47.85 GB Label- Music

Windows does'nt even recognise the remaining 100GB of written data!
Instead next to the 3 partitions listed above, it shows 97.13GB as free space!? How come?

(Refer image: Imageshack - diskmgmtsatahddalone)

I'm really really worried with this thing and dont want to go through the pain of transferring all this 100GB of data to other HDD's (which i sure dont have access to and no more space on the other partitions as well! )
Pls. help me find a way to make windows recognise the remaining two NTFS partitions....

Thanks!