Seems like just the flash ZIP file is broken, possibly due to the sdcard/0 folder??
This tool is super awesome !!!!!!!!!!! No more touching apk files by myself.
Btw I recommend using 7Zip to open the zip file and include under the "app" folder the apk file.
Did anyone notice that sometimes when the phone is charging you get the "stock" vertical battery icon and minutes later changes back to the one you moded?