After a conversion from FAT to NTFS or simply because the permissions are broken and you want to reset them (for Program Files and Windows folders), you can use this tricks to get their default (in Windows XP): http://support.microsoft.com/kb/237399.
To apply the default permission settings, run this command (from an administrative account):
secedit /configure /db %SYSTEMROOT%securitydatabasecvtfs.sdb /Cfg "%SYSTEMROOT%securitytemplatessetup security.inf" /areas filestore
Note that after you run this, SQL Server 2005 service (if it was previously installed) doesn’t start anymore. You need to give permission to the SQL Server user (or Network Service) to read/write to the %ProgramFiles%Microsoft SQL ServerMSSQL.1MSSQL folder.