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:
- (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.
- 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:
- Shut down the Mac Mini.
- Unplug the computer's power cord.
- Wait 15 seconds.
- Attach the computer's power cord.
- 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
-->(2)FW800 HDD DOCK-->FW800 CF Reader.