Yeah, are you starting from a fresh extract of the game? If a previous mod failed to apply then it leaves the game in a broken state, you need to extract it back out.
Ideally the mod engine would detect that it failed in some way, and revert, or the revert code could somehow be protected. You can delete the files folder copy the backup folder and name that copy files, and that does a revert, or i find it easier to wipe the folder and extract again.