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I have a 2012 Mac Mini with 2 x 3TB Seagate GoFlex Desk external hard drives. Both drives have their own power supplies and work perfectly.

I use both Mac OS X and Windows7 on the Mac for different reasons. Both boot and work fine.

The only problem is neither Mac OS X or Windows will boot while the two USB drives are connected. I must disconnect the USB cables, boot and reconnect them. Then all works fine.

It's rather annoying since this is mostly a Media Centre and you really don't want to be playing with cables every day, and I don't leave my stuff on over night.

Can anyone help?

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The OS may be trying to boot to the external drives. Hold down the command key while it boots to have it show a list of bootable devices. – jmreicha Jun 19 '12 at 19:22

The MacMini may be trying to boot from the connected drives and getting stuck. Go to System Preferences -> Startup Disk and select your internal boot drive. Then just close System Preferences or press "Restart..." button to test.

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Both jmreicha (with an error) and Daniel Tracy have good suggestions. Mr. Tracy's suggestion is the preferred method for long-term stability (the selection in System Preferences will stick better and should be set once everything is working properly). jmreicha should have said hold down the option key during startup however, not command (and you generally keep holding option until all, or at least the desired boot volume shows up in the list, as different devices/interfaces take different amounts of time to load here).

Also, this could be a something else... 'power related' possibly. What I would try in order of precedence:

  • reset PRAM* & change cords:
    1. (hold down command-option-p-r during startup, you will hear the startup chime a second time if it worked).
      *NOTE: You must unplug all peripherals except mouse, keyboard, and monitor for this to work properly.
    2. Rearrange cables/cords:
      • unplug all usb cables (should already be done from part 1.) and plug them into different ports if possible (both on the Computer and HD ends)
      • Change which electrical outlets the power supplies are plugged into (low priority, but has worked).
  • you could daisy chain the drives together by plugging the second drive into the other instead of having them both plugged directly in to the Mac Mini (not ideal for bottlenecks) if possible to see if that has any effect (first try one as the 'hub' then the other).
  • Reset the SMC:
    1. Shut down the Mac Mini.
    2. Unplug the computer's power cord.
    3. Wait 15 seconds.
    4. Attach the computer's power cord.
    5. Wait 5 seconds, then press the power button to turn on the computer.

I've had my current setup just stop working multiple times with multiple MacBook Pros and the above have seemed to do the trick (in combination when none of them worked alone):
USB-->Hub in Monitor
-->4 different USB devices
FW800-->Quad-Interface HUB in HDD Enclosure
-->(1)FW400 Superdrive
-->(2)FW800 HDD DOCK-->FW800 CF Reader.

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