This is not site to site transfer.
I downloaded 100 megs (files/folders) from Site A. Then I uploaded to Site B (new server).
After the upload, all permissions were messed up. Even if I only upload one file, the permissions will not be correct and appear randomly generated.
Look at the jpg and you will see that many .php files have various permissions set on them.
<edit>The permissions will be incorrect even if re-uploading to a new dir in Site A.
</edit>