All the problems I described seem to have been red herrings. I have now found both the problem and a solution. it was as in most of these cases both unexpected and simple.

I had installed Norton Systemworks 2003 on my windows partition which includes a limited version of Go-Back. Go Back makes changes to the master boot record which in turn lead to all of the problems outlined above. My problem was of course that when I got to the stage where i was given the message that i had to disable Go-Back I was already unable to boot windows and so could not do it by the normal route. In the end I found the link shown below on the Norton/Symantec website which referred me to a program (gb_prog.exe) on the Systemworks CD ROM which can be run from a system disk and which reverses the changes made to the MBR and so allows the FDISK /MBR command to work normally. Once this was done, everything was fine. Windows booted normally and i will now be able to use the copy of partition magic which i bought as part of my desparate search for a solution to resize the fat32 partition, erase my red hat and then install a new distro on my shiny new seagate 160Gb hard-drive which was also bought as part of this saga.

I hope this is useful to people.

=====================================

Go Back link (and full text)

http://service1.symantec.com/SUPPORT...=&osv=&osv_lvl

How to remove changes that GoBack makes to the boot sector and partition tables of a computer

Situation:
When you start your computer, GoBack no longer launches correctly. You may also be unable to access your hard drive.

Solution:
Damage or changes to a computer's boot record may prevent access to the hard drive, causing the computer to stop responding or preventing access to information. By design, GoBack works with the boot record to provide system restoration capability. To troubleshoot problems with the boot record, you may want to remove the changes that GoBack has made.
--------------------------------------------------------------------------------
Notes:
The following instructions require a computer that can successfully start Windows 98/Me in order to create a Windows Startup disk. This computer does not have to be the computer you are trying to remove GoBack changes from.
Gb_prog.exe can be located in the GoBack installation folder (C:\Program Files\GoBack is the default location). Gb_prog.exe can also be found on the Norton SystemWorks CD in the \Support\GBTools folder.
If you have Norton SystemWorks 2002, follow the instructions in the document How to extract the Gb_prog.exe file from the Norton SystemWorks 2002 CD to extract the Gb_prog.exe file.
--------------------------------------------------------------------------------
To remove the changes that GoBack made to the boot record

Create a Windows Startup disk under Windows 98/Me. For more information, see the document How to create a Windows Startup disk.
Copy the Gb_prog.exe file to the Windows Startup disk. If there is not enough room to copy Gb_prog.exe to the Windows Startup disk, then copy Gb_prog.exe to a separate floppy disk.
On the computer that you want to remove the GoBack changes from, insert the Windows Startup disk and then start the computer. The computer has finished starting when you see an A:\> prompt and a blinking cursor.
Insert the disk that has the Gb_prog.exe file.
Type gb_prog.exe /u and then press Enter.
The utility removes the changes that GoBack made to the boot sector and the partition table and further troubleshooting can proceed. If this method does not successfully remove GoBack from the boot record, then see the document Cannot start Windows after installing GoBack.
--------------------------------------------------------------------------------
Note: This process does not entirely remove the GoBack program. Use the Add/Remove Programs utility in the Windows Control Panel to remove the rest of the GoBack program.
--------------------------------------------------------------------------------

[This text just to help people find this solution if doing web search: Cant boot windows but need to disable go-back. Go back changes mbr and prevents fdisk /mbr working. Error message says disable go-back but I cant start windows.]