Peter,
Hopefully I caught you before you formatted and fdisked, etc...
The repair was a good idea. But, there are some limitations to what it can do for you. I'll try and explain a bit on what happens, and maybe figure out a way for you to keep your mathcad program.
The repair option goes through your windows files and system files to see if any are corrupt or missing. This usually works pretty good, but the limitation is when you install other software. Quite a few of the files that it will go through and change are called .dll's, or direct link libraries. A direct link library is a file that is used on several programs, not just one. If it notices that an installation of another program has changed the .dll to another format than what windows had installed, it will wipe out your new .dll and replace it with the old version from the windows cabinet (.cab) files. New installations use the original windows .dll files and enhances them, for easier programming. Imagine having a plc program setup with subroutines. The .dll file is a subroutine, but in windows, if it comes across a piece of code that it's not using, or does not recognize, it will skip over it. You can see how easy it is for the programmers to go through and just add to the original code, instead of having to literally do thousands of lines over again.
What you can try and do for your machine, figure out what programs are acting flakey and reinstall them. This is called a 'dirty install' and just may be able to get you past your issue. The 'dirty install' will do the same as the windows repair, it will scan the files that it needs, see which ones have been altered, and change anything that does not meet the installation. I have done this on several windows machines, with a pretty good success rate.
IF that does work for you, to convert to ntfs, just use this command from start/run... (assuming your hard drive, or drive that you want converted is c: )
convert c: /fs:ntfs
If, for example, it's d:, just use convert d: /fs:ntfs, etc...
It will convert from fat32 to ntfs for you the next time you restart. It will not lose any data. The only warning I can give you on this, is once you convert to ntfs, you cannot reinstall a fat32 operating system easily. Usually involves a low level format... but that's another story.
Hope you're able to salvage all your stuff, Pete.
Hoot