The system boot failure happens when your PC can't find anything to boot off, ie. no hard drive, so will ask for a CDROM or floppy disk.
It could be that your hard drive has become corrupt, but that would normally be a permanent error. If it does manage to boot windows will often find a corrupt file and sometimes miraculously recovers itself.
Have you checked all your cables are firmly attached? A loose data or power cable to your hard drive could cause this problem.