Bootsect.exe is explained on this Link Removed site. It tells the system to look for a Win 7 type boot system if you use the /NT60 switch. But you need access to the utility first.
Because of your system setup, it is very hard to tell what might be going on with the system. If your Windows partiton has been wiped, nothing will make it boot. If you decide it might help, you could download and burn the bootable versions of either Partition Wizard or G-Parted to check your drive's partition. A picture of that window attached here would help us.
Are these discs you have meant to be run by themselves, or as part of the System reimage utility?