All done.....MS support pages are actually quite neat......its all there if you search.
One of the two versions of OS boots were actually the remnents of a failed XP install (during the NTLDR missing problem) sitting as a line in the boot.ini file. Once deleted as per ms instruction the system boots nicely and now even asks me to log onto my account.
I had to get a new KVM switch that could handle multiple OS (one PC is 98se the other XP) and emulate the key board and mouse during boot.
I updated Win XP which had an update for my X52. This promptly caused the profiler to reject my existing profiles and any new ones I created.
The Saitek help sit described a very arduous work round which was followed and the profiler works OK now.
My system is till fat 32. There is no separate ntfs partition unless XP created it for its own OS files and is hiding it's existance somewhere. (maybe that big green block at the end of the defrag bar)
Once everything else has stabalised I'll convert the whole thing to ntfs although I do not see any benefit (to me) in doing so.