This happen when i was using WIN2k server, WIN2k pro.
My OS crash, the only way i can troubleshoot was by boot disk.
Firstly. i backup all mysql\data\ to another tune backup hard disk. Format the PC.
When MySQL installs new, i actually copy and paste the data folder. But remember.... For safety purposes I generate the OUTFILE database1.sql then delete the selected database, create new database and load database1.sql. The data was new and brand new and safe.