No, dont use FAT32 -you will kill your data much quicker than you can imagine, believe me. But you will discover how windows badly work in FAT32 by yourself. It's not W95...
You ended up in the 'funny' problem of NTFS that plagued many, myself included. Usually you can access the NTFS unit with a live linux CD, or a linux boot.
Apart that, NTFS it is usually quite stable in windows.
Install linux in your machine, also... and make a few partitions too
