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I have partitioned a 1TB external drive into three independent drives i.e. iTunes, Docs, Video. In Time Machine I have set the Preferences to only back up the internal drive (which contains my apps, settings, etc - a total of 45.58 GB). When the 1TB partitioned drive is on, Time Machine tries to back up all three of them + my internal drive resulting in the typical "too large" error message.

NOTE: Even when turned on, the other three drives don't even show up in the "Options" window where you "Exclude these items from back-ups". They do, however, show up in the "Select Disk" window.

When the 1T partitioned drive is off, Time Machine performs as expected i.e. backs up only the internal drive.

Is there a way of ensuring that only the internal drive is backed up?

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I cannot reproduce these conditions (I have an external drive with a data partition which is excluded from TM's settings, which shares the same physical drive as the TM backup). I have voted this question up, though. – user3463 Sep 13 '11 at 7:49
    
How is your external drive connected? For me (10.7.1) TimeMachine automatically adds any attached USB drive to the exclude list (and I cannot remove those entries). This might be different for FireWire drives though... – barbaz Sep 15 '11 at 11:03

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