When you install Windows with multiple drives, the boot files may not have been placed where you would think.
You could try reinstalling now to see if it would take. If you do not want to reinstall, you could try looking at the drive with either Diskpart from the command prompt to verify the configuration, or download and burn a third party Disk Management software like Partition Wizard. Burn it and boot to it to look at the drive configuration. If you could get some type of picture of the configuration, that might help.
Partition Wizard Bootable CD allows user to manage partition directly with partition manager bootable CD.
Possibly the active partition was on the drive that had the bad cable. Now, the other drive does not have the boot system on it, but just guessing. Maybe replacing the SATA cable would solve the problems. If the second drive did have the boot files, you would want to set it primary in the bios. I suppose the IDE drive could be involved, but best to get your system set up with the entire Windows install on one drive.