I was doing a fresh install of my development site to 1.2.3 in a new directory but when I was installing it it asked me if I wanted to overwrite some files. This doesn't make sense to me, surely all files should be unique in a fresh install and if some are being overwritten wouldn't this affect performance?
In some cases FileZilla experiences delays which results in the odd file being retransmitted but this only happens for a handful of files out of the whole package.
If it is asking to overwrite all files then you haven't cleared the old/original files from the server or are uploading to an existing directory.
Personally I don't use FileZilla due to the first point - it was causing too many problems.
I exclusively use WinSCP.