Why does plugging in an eSATA cable cause Ubuntu to forget about an internal drive?

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http://askubuntu.com – When I plug an eSATA cable into the external eSATA port that is attached to my motherboard (Fatal1ty Z68 Professional Gen3), the internal SATA drive that my root partition is on is seemingly disconnected (most all programs begin to crash immediately). If I attempt to boot into Ubuntu's recovery mode with the cable plugged in, it fails after trying to find the internal drive by UUID. Note that this happens even if only the cable is plugged in. The cable and external drive works fine when I boot into Windows. What might my next steps be to diagnose this issue or, better, fix it? (HowTos)