I am able to easily reproduce the auto-eject problem during Carbon Copy Cloner operations even while booted up in Safe Mode. However, I did run the procedure you suggested, do you see any kernel extensions in the diffs I captured?
# used AWK to strip out all but column 6 in the original files
diff full.txt safe.txt
25a26
> com.apple.driver.AppleIntelLpssDmac
29d29
< com.apple.driver.AppleIntelLpssDmac
36d35
< com.apple.driver.AppleHSSPISupport
38a38
> com.apple.driver.AppleHSSPISupport
45a46
> com.apple.driver.XsanFilter
48d48
< com.apple.driver.XsanFilter
51a52
> com.apple.driver.AppleFileSystemDriver
63a65,66
> com.apple.iokit.SCSITaskUserClient
> com.apple.iokit.IOUSBHIDDriver
73d75
< com.apple.driver.AppleCameraInterface
75,77c77
< com.apple.driver.AppleSMCLMU
< com.apple.iokit.IOHDAFamily
< com.apple.driver.AppleHDAController
---
> com.apple.driver.AppleSMBusPCI
83,91c83,86
< com.apple.driver.AppleThunderboltIP
< com.apple.driver.AppleHWAccess
< com.apple.kext.OSvKernDSPLib
< com.apple.iokit.IOAudioFamily
< com.apple.vecLib.kext
< com.apple.driver.DspFuncLib
< com.apple.driver.AppleHDA
< com.apple.iokit.IOSurface
< com.apple.driver.AppleIntelHD5000Graphics
---
> com.apple.driver.IOPlatformPluginLegacy
> com.apple.driver.ACPI_SMC_PlatformPlugin
> com.apple.driver.AppleGraphicsControl
> com.apple.driver.AppleMuxControl
92a88
> com.apple.driver.AppleGraphicsDevicePolicy
96,103c92
< com.apple.driver.ApplePlatformEnabler
< com.apple.iokit.IOUserEthernet
< com.apple.driver.AppleUpstreamUserClient
< com.apple.iokit.IOSerialFamily
< com.apple.iokit.IOBluetoothSerialManager
< com.symantec.kext.ndcengine
< com.symantec.kext.ips
< com.apple.driver.AudioAUUC
---
> com.apple.iokit.IOSurface
106,110d94
< org.virtualbox.kext.VBoxDrv
< org.virtualbox.kext.VBoxUSB
< org.virtualbox.kext.VBoxNetFlt
< org.virtualbox.kext.VBoxNetAdp
< com.symantec.kext.SymAPComm