Wow sometimes it's hard to understand you, Taipan.
E.g. I'm TOTALLY confused how a "program" can read the right stuff IN WINDOWS, when Windows doesn't see it correctly!?!
Anyway, since/if you're sure that it's a problem with the HDD that is preventing Windows from seeing the partitions correctly, you're going to HAVE TO FIX IT OUTSIDE OF WINDOWS. (I'm hoping that you already knew this, right?!?)
So, you're going to need something BOOTABLE to scan & fix it, and if you want to be REALLY safe, IMAGE IT BEFORE you try to fix it (any further.)
I use PartitionMagic for such things, but you can shop around to find any of many suitable utilities that can be BOOTED to once burned on CD that will image, or scan & repair a Windows-formatted, but damaged drive/partition.
Does that help you any?!?