. What is the difference between partitioning and formatting

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Formatting is basically deleting the entire drive (kinda - you can still recover the data if you do it on accident as long as you have another drive to boot to and you don't install anything on the newly formatted drive. I can't remeber the name of the program that I've used to do this....) anyways, that's not your question.
Partitioning is making your BIOS think you have two hard drives (or however many partitions you add - 2 partitions = 2 (virtual) hard drives) If you add a partition with a MBR (master boot record) then you can add another operating system to that partition, ie. Win XP on your first partition & Linux on your second. When you partition your drive, it will add another Drive letter. So, if your HDD is C:, then the partitioned drive will be D:.
Steve touched on this a little. If you're slaved hard drive has a master boot record, that may be where you are getting the problem. A MBR is usually the first however many sectors of a HDD that contain the boot-up information for your PC's OS. W/o this, your BIOS won't know where to find the OS.
Now, this is where this advice might not prove to help. Usually, if you have 2 boot options, it will prompt you which one you want to run, however, if you didn't reformat the slaved drive initially, or if you have formatted it and placed a MBR on it (which im unsure if you can do w/o installing an OS) then it might be confusing your pc and causing an error. I would delete the MBR on the
SLAVED HDD.
One other thing, if you have SMART HDD Monitoring on your Mobo, turn it off. I have it on mine and it always reports an error. My HDD is brand new and I know thiers no problem w/ it. Sorry this was so long, hop eit helps.