I had the same problem when I had red hat and win98 on the same machine. What happend to me was somhow the two partitions overwrote eatchother. Suddenly lot's of my documents were corrupteded and linux wouldn't even start. I used a partitioning program shipped with the cd (fips or something like that?). Anyway, it crashed my disk and from now on I'm only using partition magic. It's a safe bet.

If you encountered problems it would be wise to backup your disk as soon as possible. Don't expect things to work out like I did.....