Copy files: Skip Identical, followed by Replace All

When I have to copy a large set of files and it found a identical file, it ask if I want to replace I choose ignore all, then it found a not identical and I choose replace all. Now it going to replace all the files, including the identicals where I choose to ignore.
When is a local file copy it´s ok, but when is over FTP, is a lot of extra bytes.

It shouldn't, as far as I know.

Are the files being replaced definitely identical?

("Identical" in this context means the same size and modified timestamp. They have to be exactly the same for it to skip the files.)