[One (M7) Q&A, Help & Troubleshooting] LibertyMarine:
Okay.. if you have a stock backup.. you are good to go.. Now since you have TWRP you should be able to use this BackUp to PC tool to move your backup to your PC(this tool works only with android filesystem 4.2+):

http://www.mediafire.com/download/rx4h29bdk4v4b45/BackUpToolBox-ENGLISH.zip

And if you think it's a virus.. here's the source code:

::===========================================
::This is Version 4.0 of Android BackUp to PC
::English Version
::===========================================
@echo off
title Android BackUp To PC
cd resources

:startProcedure
echo ===============================================================================
echo Welcome to Android BackUp To PC ToolBox
echo Instructions: -Only CWM and TWRP are supported
echo -The Creator of this device is not responsible for any kind of
echo damage caused by this tool to your device
echo -Enable UBS-Debugging!
echo -Press a key to boot into the Recovery
echo ===============================================================================
adb devices
pause
adb reboot recovery
echo Waiting for Device...
echo\
echo ===============================================================================
echo Further Instruction: -Wait until your device has booted into the recovery
echo -Then do mount the /data and /system partition
echo -If you created the BackUp with TWRP press: T
echo -If you created the BackUp with CWM press: C
echo ===============================================================================
set /p pfadUserChoice=
if %pfadUserChoice% == C goto clockWorkMod
if %pfadUserChoice% == T goto teamWorkModRecovery
goto beenden

:teamWorkModRecovery
echo ===============================================================================
echo Now write the directory, where you want to BackUps to be stored to, in the
echo space down below:
echo (for example D:\Users\Name\BackUps )
echo ===============================================================================
set /p computerDirectory=
echo Now type the particular folder name of the BackUp. If you want to copy every
echo BackUp then simply press enter!
set /p backUpDirectory=
set backUpDirectoryFinalTWRP=/data/media/0/TWRP/BACKUPS/%backUpDirectory%
echo The Files are copied when you execute the next order.
echo Von: %backUpDirectoryFinalTWRP%
echo Zu: %computerDirectory%
pause
adb remount
adb pull %backUpDirectoryFinalTWRP% %computerDirectory%
echo If no file was skipped everything worked fine!
echo Conclude!
pause
goto ende

:clockWorkMod
echo ===============================================================================
echo Now write the directory, where you want to BackUps to be stored to, in the
echo space down below:
echo (for example D:\Users\Name\BackUps )
echo ===============================================================================
set /p computerDirectory=
echo Now type the particular folder name of the BackUp. If you want to copy every
echo BackUp then simply press enter!
set /p backUpDirectory=
set backUpDirectoryFinalCWM=/data/media/clockworkmod/backup/%backUpDirectory%
echo The Files are copied when you execute the next order.
echo Von: %backUpDirectoryFinalCWM%
echo Zu: %computerDirectory%
pause
adb remount
adb pull %backUpDirectoryFinalCWM% %computerDirectory%
echo If no file was skipped everything worked fine!
echo Conclude!
pause

:ende

Using to tool is easy.. it's full of instructions and you should be able to use it without any problems. Now then you BackUp'ed your BackUp to your PC and now push the rom.zip to your phone with this command:

adb push "C:\directorytorom" /data/media/0

this should copy the whole content that's in your directory to your sd card..

now flash the ROM and look if it's having the same issue again.

No I think i don't need a pic.. and calm down.. It's very unlikely to be a hardware problem...

if this helped.. feel free to hit that thanksbutton down below :)