[Nexus 6  General] JW09I4:
Ensure you're using the most recent CF Auto Root version from the link a few posts up.

Have you tried performing the root again via fastboot boot cf.img? If so, I do know I saw that for a brief second the first time I ran cf after flashing 6.01 [it's due to Verity], however after re-flashing 6.01 again, and re-rooting it never reappeared.

I can't confirm exactly which flashed partition solved it, as I was customizing my Flash.bat and ran it through 5 or 6 times before I was satisfied with it; Most likely the boot or system partition (possibly the bootloader?). I would try reflashing the bootloader and boot partition and see if that solves it.

Also, cf will cause a boot loop for a few boots (on mine it was 2)... it's important to not interrupt that process and allow the device to fully boot into android once issuing the fastboot command.

You'll need to unlock your bootloader before hand by entering the bootloader options and issuing the command fastboot oem unlock. You need to physically interact with a confirmation on the device once the command is issued. Its recommended doing this prior to booting into Android, as once you unlock or relock the bootloader, the device performs a factory reset.

You may get an error that you'll need to manually enable the option within Settings - Developer Options, at which point simply skip your way through the first time setup. You'll need to go into Settings - About Phone and tap on Build Number seven times to enable the Developer Options option in Settings.

I personally would recommend simply flashing the latest firmware prior to booting the new device, as it's quicker and bypasses the need to do the above to unlock the device (provided you don't boot after flashing until you've unlocked the device). You'll want to ensure you have Android SDK installed, with the latest USB drivers from the SDK installed (it's recommended to add the platform-tools directory to the environment path of your PC, which allows you to utilize fastboot and adb from any cmd/powershell terminal). You can save the following as a .bat file, which will flash the firmware, flash a custom recovery (TWRP is what I use, but there are others), unlock the bootloader, and boot CF Auto Root :

Flash.bat

(see post 187 for steps)

::##[[-----> Nexus 6 Firmware Flash <----]]##::

@echo off
echo.
echo.
echo.
echo ...Flashing Bootloader...
@echo on
fastboot flash bootloader bootloader-shamu-moto-apq8084-71.15.img

@echo off
echo.
echo.
echo.
echo ...Rebooting Bootloader, waiting for 7 seconds...
@echo on
fastboot reboot-bootloader

@echo off
ping -n 7 127.0.0.1 >nul

echo.
echo.
echo.
echo ...Flashing Radio...
@echo on
fastboot flash radio radio-shamu-d4.01-9625-05.32+fsg-9625-02.109.img

@echo off
echo.
echo.
echo.
echo ...Rebooting Bootloader, waiting for 7 seconds...
@echo on
fastboot reboot-bootloader

@echo off
ping -n 7 127.0.0.1 >nul

echo.
echo.
echo.
echo ...Flashing Recovery...
@echo on
fastboot flash recovery recovery.img
@echo off
echo.
echo.
echo.
echo ...Flashing Boot...
@echo on
fastboot flash boot boot.img
@echo off
echo.
echo.
echo.
echo ...Flashing System...
@echo on
fastboot flash system system.img
@echo off
echo.
echo.
echo.
echo ...Flashing Cache...
@echo on
fastboot flash cache cache.img
@echo off
echo.
echo.
echo.
echo ...Formatting Cache...
@echo on
fastboot format cache
@echo off
echo.
echo.
echo.
echo ...Formatting UserData...
@echo on
fastboot format userdata
@echo off
echo.
echo.
echo.
echo ...Flashing TWRRP Recovery...
@echo on
fastboot flash recovery twrp-2.8.7.1-shamu.img

@echo off
echo.
echo.
echo.
echo ...Unlocking Bootloader...
@echo on
fastboot oem unlock
@echo off
echo.
echo.
echo ...Follow device's on screen instructions...
echo.
echo.
echo ***--- Once device verifies it's unlocked, with Status Code: 3, press any key to continue ---***
echo.
echo.
pause

echo.
echo.
echo.
echo ...Booting CF Auto Root...
@echo on
fastboot boot CF-Auto-Root-shamu-shamu-nexus6.img
@echo off
echo.
echo.
echo ***--- CF Auto Root is rooting device, once fully completed, press any key to exit ---***
echo.
echo.
echo ...CF Auto Root will cause the device to boot loop a few times, DO NOT INTERRUPT THE PROCESS...
echo.
echo.
pause

:: #--- Command to only update firmware ---#::
::-------------------------------------------::
:: fastboot -w update image-shamu-mmb29s.zip