At first you should check towelroot thread
. Its simplest way to get root.
But the flashtool should start from the beginning. close flashtool program, install drivers from \flashtool\drivers. kill all processes that use adb.exe (all instances of adb.exe, pc compagnion in task manager) and start over.
I suggest you check what condition is the usb cable. Once cheap cable was fault of brick my xperia S.
PS. You do not need to have enabled debugging for flashing.