[Motorola Photon 4G] i7vSa7vi7y:
I had problems like this before so I modified the root batch program.

Right click on the root.bat and choose edit. Ctrl + A to select all and then backspace to delete all the text. Copy this into there and save. All I did was put multiple pauses where the phone needed to reboot so hit space bar whenever your phone successfully is at your home screen. I like to give it a little bit of time to load and what not. Let me know your outcome.

@echo off
echo based off bliss' moto exploit for the droid 3 published here http://vulnfactory.org/blog/2011/08/25/rooting-the-droid-3/
cls
color 0A
echo.
echo.
echo.
echo.
echo.
echo.
echo.
echo.
echo The Android Creative Syndicate
echo.
echo Presents to you
ping -n 2 127.0.0.1 > nul
cls
echo.
echo.
echo.
echo.
echo.
echo.
echo.
color 0C
echo One Click Root
echo for the Moto Photon 4G
ping -n 2 127.0.0.1 > nul
color 0A
echo.
echo.
echo Special shoutout to
echo.
echo. Bliss
echo.
echo.
echo.
pause
cls
echo.
echo.
echo.
echo.
echo.
echo.
echo.
echo You need to enable usb debugging first
echo Go to settings - applications - development
color 0A
ping -n 2 127.0.0.1 > nul
color 0C
ping -n 2 127.0.0.1 > nul
color 0C
echo.
echo.
pause
cls
echo.
echo.
echo.
echo.
echo.
echo.
echo.
cls
adb.exe kill-server
adb.exe start-server
COLOR E0
echo Getting temp root
pause
adb shell rm /data/local/12m.bak > NUL
adb shell mv /data/local/12m /data/local/12m.bak > NUL
adb shell ln -s /data /data/local/12m > NUL
echo Will Reboot phone
pause
adb reboot

echo.
echo RE-boot-en
COLOR 47
adb kill-server > NUL
adb wait-for-device > NUL
adb wait-for-device > NUL
echo.
echo Hackin Things
COLOR A0
pause
adb shell rm /data/local/12m > NUL
adb shell mv /data/local/12m.bak /data/local/12m > NUL
adb shell rm /data/local.prop.bak > NUL
adb shell mv /data/local.prop /data/local.prop.bak > NUL
adb shell echo "ro.sys.atvc_allow_netmon_usb=0" ^> /data/local.prop
adb shell echo "ro.sys.atvc_allow_netmon_ih=0" ^>^> /data/local.prop
adb shell echo "ro.sys.atvc_allow_res_core=0" ^>^> /data/local.prop
adb shell echo "ro.sys.atvc_allow_res_panic=0" ^>^> /data/local.prop
adb shell echo "ro.sys.atvc_allow_all_adb=1" ^>^> /data/local.prop
adb shell echo "ro.sys.atvc_allow_all_core=0" ^>^> /data/local.prop
adb shell echo "ro.sys.atvc_allow_efem=0" ^>^> /data/local.prop
adb shell echo "ro.sys.atvc_allow_bp_log=0" ^>^> /data/local.prop
adb shell echo "ro.sys.atvc_allow_ap_mot_log=0" ^>^> /data/local.prop
adb shell echo "ro.sys.atvc_allow_gki_log=0" ^>^> /data/local.prop
adb reboot

echo.
echo deleting all yo ****
COLOR E0
pause
adb.exe wait-for-device > NUL
adb.exe wait-for-device > NUL
adb.exe remount
COLOR B0
adb.exe push rootsetup /data/local/tmp/rootsetup
adb.exe shell chmod 755 /data/local/tmp/rootsetup
adb.exe shell /data/local/tmp/rootsetup
adb.exe shell rm /data/local/tmp/rootsetup
adb.exe shell sync

echo Copying files onto phone...
adb.exe push su /system/xbin/su
adb.exe push Superuser.apk /system/app/Superuser.apk
adb.exe push busybox /system/xbin/busybox
adb.exe push remount /system/xbin/remount

echo Setting permissions...
adb.exe shell chmod 755 /system/xbin/busybox
adb.exe shell chmod 755 /system/xbin/remount
adb.exe shell chown root.shell /system/xbin/su
adb.exe shell chmod 6755 /system/xbin/su
adb.exe shell ln -s /system/xbin/su /system/bin/su

echo Installing busybox...
adb.exe shell /system/xbin/busybox --install -s /system/xbin

echo Cleaning up files...
@ping 127.0.0.1 -n 6 -w 1000 > nul
adb.exe shell rm /data/local/tmp/*
adb.exe reboot

echo "You should have root!"
COLOR D0
ping -n 1 127.0.0.1 > nul
COLOR 90
ping -n 1 127.0.0.1 > nul
COLOR B0
ping -n 1 127.0.0.1 > nul
COLOR A0
ping -n 1 127.0.0.1 > nul
COLOR E0
ping -n 1 127.0.0.1 > nul
COLOR C0
ping -n 1 127.0.0.1 > nul
COLOR D0
ping -n 1 127.0.0.1 > nul
COLOR 90
ping -n 1 127.0.0.1 > nul
COLOR B0
ping -n 1 127.0.0.1 > nul
COLOR A0
ping -n 1 127.0.0.1 > nul
COLOR E0
ping -n 1 127.0.0.1 > nul
COLOR C0
ping -n 1 127.0.0.1 > nul
COLOR D0
ping -n 1 127.0.0.1 > nul
COLOR 90
ping -n 1 127.0.0.1 > nul
COLOR B0
ping -n 1 127.0.0.1 > nul
COLOR A0
ping -n 1 127.0.0.1 > nul
COLOR E0
ping -n 1 127.0.0.1 > nul
COLOR C0
echo.
pause
adb.exe kill-server
goto:eof