Partitions visible but cannot boot

Two partitions are visible and data intact (can see this by using testdisk software). These partitions are both NTFS - the first is 5GB and the second is 20GB. Have tried "fidsk /mbr", have tried rebuilding mbr using testdisk software. However when I now go to Windows XP setup using XP bootdisk it only shows just one partition as FAT16. Don't know what to do anymore, please help.
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I'm not sure the extent of what may be going on here where you need a bootdisk but if your using an xp setup disk it sounds like you are trying to save your data and reinstall you OS.  If that is the case, I have done and recommend the following.
1. Run setup to install XP (pro I assume).  After loading device drivers, Do not run repair
2. It will say that it has detected an previous installation.  You want to have it delete the windows directory and reinstall there.  Do not format any part of the drive or write a new installation over the existing directory.  
3. It will look like a new installation and eventually you will need the XP CD key and install the drivers.
4. Once it does boot, you docs and other various items will still be there.  Most of your applications will need to reinstalled, but your data should be intact.

The nice thing about this that you have a fresh install with all your data intact.  This recommendation is based on what you wrote.  If you have different intentions please specify.
Boot from a Xp bootable Cd...First Use " C"  to  delete partition....then in unpartitioned space again format it in... NTFS
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Is your system an old system?

A Disk Drive Overlay is used to overcome a BIOS drive size limit.
One sometimes uses it to put a large capacity hard disk in an older system that does not recognise the full size of the hard disk.
When your machine needs and has an overlay, and your machine BIOS is set to first try boot from FLOPPY or CDROM and you do so, the overlay is bypassed because you do not load the overlay from hard disk. Overlay software normally gives you an option to boot from floppy, but does that only after it got the options screen while initiating the bootprocess from HARD-DISK.
In other words, if you boot straight from a floppy, you may have bypassed an overlay, and the hard disk may inexplicably become invisible to DOS... or show a size of 504MB only...
Windows 98's FDISK not giving you the fat 32 option on a high capacity hard disk can be a giveaway symptom too...
(There are other ways to find out if there was/is an overlay which is discussed later in the thread... This symptomatic info is briefly mentioned here, since you want to load the overlay during boot time if your disk uses an overlay.)

Some warnings about fdisk /mbr
It is often recommended that one use fdisk /mbr to sort out some problem.
But, you had better known about the possible dangers.
FDISK /MBR can cause serious problems when you
#are using a boot manager for multi OS booting
#have more than 4 partitions
(have recently ran a few trials, and it's true)
#require disk management software (overlay).
#use goback or second chance (or similar)
#use a laptop with a boot util for swappable cdrom and floppy bays
#have a machine wich has a tattoo bios copied on the drive.

The above information can be found more in
Corrupte partion will show different information on different OS.
Even the fresh format will not give you out the solution.
better do the backup of all data from the OS, which is showing the full information of the hardisk.
And then repartion the entire disk.

Most of the crititcal partion problem can't be solved as easier.
It may solvable in some scenario, or it can be corrected by experts.

srini ms
nobusbiljart fanCommented:
was any of your partitions set to active? if not, you cannot boot from them.
To set them, use a bootable floppy (even for win98) and set the partition to active.

Here is a freeware which maybe useful for anybodyto do diagnostic and troubleshooting
Ultimate Boot CD:
What is the WinUBCD?? WinUBCD is a bootable CD which contains software that allows you to repair/restore/diagnostic almost any computer. All software included in WinUBCD are freeware utilities for Windows®. WinUBCD uses Bart's PE© which is how the CD boots into a Windows® environment with network support. Perfect for recovering deleted files on your harddrive without accidentally overwriting them or scanning a virus infected system.

This project currently has 50+ utilities included in the download. Anti-Virus, CMOS password recovery, password finders, file recovery, Networking tools, CD burning software, MBR backup and recovery, etc. types of applications are all included in the download. Please visit the "List of Tools" page for a complete list of what is included in the project.

Author: UltimateBootCD.Com
Software: Ultimate Boot CD/WinUBCD
Program Type: Free!
Download Page!
File Size: 69.9 Mb
Platform: Windows all 95/98/Me/2000/XP
Sorry the new download site is  for the WinUBCD
ma701sssAuthor Commented:

I have data on the partitions, so I can't just format everything and start again. I have used Partition Table Doctor and Testdisk and they both find all partitions, correct sizes, starting positions, etc. It's just that when I go into Windows XP setup in order to re-install onto one of the partitions, it just shows one large partition (FAT16). Even if I attempt to install on here just to see what the next screen says, it says that the partition is damaged, etc. I don't understand why it is so difficult to repair if all the partitions are there with data on them and everything else seems to be fine. I can ever set active partitions and boot to the partitions. Windows XP just can't see the partitions in XP setup when I boot from the XP CD.
Aside from the comment above that I posted, There may not be much else you can do. Sorry
nobusbiljart fanCommented:
time for recovery i think. Hook the drive to the IDE cable of a working PC, and copy what you need.
>>    I don't understand why it is so difficult to repair if all the partitions are there with data on them and everything else seems to be fine   <<  it is not difficult if you have enough knowledge and tools; you can edit and rewrite the boot sectors IF you know what they must be.
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