Does Time Machine only work with external HDD's and Networks?

I have a Mac Mini that I just replaced the optical drive with a hard drive. This second HDD is formated into two partitions, with one of them being for my Time Machine backups, the other a media scratch drive.
When I try to choose this volume in setting up Time Machine, I get an error message that says, +"Are you sure you want to back up to the same disk your original data is on?"+ The message goes on to explain that +"the volume you have chosen for storing backups is on the same disk as the volume containing your data... you should back up to a volume on a different disk."+
The volume that I have selected IS on a different disk than my start-up system drive and the data to be backed up IS NOT on the same disk as the disk storing the backups. System Profiler defines my startup HDD as "BSD Name: disk0" and my second HDD as "disk1," with the two partitions "disk1s2" and "disk1s3." Mount Point for the start-up HDD is "/" and the two partitions on the second HDD are "/Volumes/Scratch Disk" and /Volumes/Time Machine." These two volumes show up as options when I "Choose Backup Disk" in Time Machine, but not the Mini's startup HDD.
Does Time Machine allow the use of second internal HDD? I have an external HDD, but it has a clone of my start-up drive on it. Thanks for any help.

Chris, excluding the other volume could certainly be the issue since the two options that I'm given for a backup volume are both on the same hard disk. The start-up system HDD is not listed. Maybe the message is referring to this, rather than to the start-up disk.
Not until after I selected "use this volume anyway," did I get to the "Option" screen to exclude items from the backup. When I selected "+" I was surprised to find the other volume, Scratch Disk, listed along with the start-up HDD as being included in the backup routine. So I selected Scratch Disk as one of the items to exclude.
As V.K. mentions, the cautionary message is rather vague as to what exactly it is referring to. Thanks.

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    1/13/13 12:21:26.021 PM com.apple.security.pboxd[1518]: CGSReleaseWindow: Invalid window 1973
    1/13/13 12:21:26.021 PM com.apple.security.pboxd[1518]: _NXTermWindow: error releasing window (1000)
    1/13/13 12:21:27.775 PM sandboxd[1658]: ([1657]) QuickLookSatelli(1657) deny mach-lookup com.apple.PowerManagement.control
    1/13/13 12:21:52.000 PM kernel[0]: disk1s2: I/O error.
    1/13/13 12:21:57.967 PM fseventsd[44]: disk logger: failed to open output file /Volumes/Big2TB/.fseventsd/0000000000048e11 (Invalid argument). mount point /Volumes/Big2TB/.fseventsd
    1/13/13 12:21:57.967 PM fseventsd[44]: disk logger: failed to open output file /Volumes/Big2TB/.fseventsd/0000000000048e11 (Invalid argument). mount point /Volumes/Big2TB/.fseventsd
    1/13/13 12:21:57.000 PM kernel[0]: disk1s2: I/O error.
    1/13/13 12:21:58.229 PM com.apple.kextd[11]: Can't create kext: invalid CFBundleVersion in identifier cache entry entry 339.
    1/13/13 12:21:58.000 PM kernel[0]: jnl: disk1s2: close: journal 0xffffff800908acc0, is invalid.  aborting outstanding transactions
    --- End Console ---
    ---- That's all folks! ----
    Any help would be great!

    The external drive is malfunctioning, or the data cable is bad, or you have another malfunctioning device on the bus, or there's an internal hardware fault.

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