I have noticed that the ftp synchronize doesn't show "hidden" files or folder (any file or folder beginning with ".") on the server. Some other ftp clients I have used does show the hidden files and I would really like to see Synchronize It! to support them too.
I don't know the specifics how the hidden files work with ftp, but by comparing the ftp logs of Synchronize It! and WinSCP, I noticed that WinSCP uses slightly different command (LIST -a) when requesting the file list.
Synchronize It!: LIST
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-rw-r--r-- 1 testu webusers 184 Aug 19 13:08 COPYRIGHT
-rw-r--r-- 1 testu webusers 4734 Aug 19 13:08 HISTORY
-rw-r--r-- 1 testu webusers 2142 Aug 19 13:08 LICENSE
-rw-r--r-- 1 testu webusers 681 Aug 19 13:08 README
-rw-r--r-- 1 testu webusers 2883 Aug 19 23:24 index.php
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drwxr-xr-x 3 testu webusers 108 Aug 22 23:38 .
drwxr-xr-x 4 testu webusers 47 Aug 19 14:37 ..
-rw-r--r-- 1 testu webusers 325 Aug 19 13:08 .htaccess
drwxr-xr-x 5 testu webusers 111 Aug 19 14:44 .pdirl
-rw-r--r-- 1 testu webusers 184 Aug 19 13:08 COPYRIGHT
-rw-r--r-- 1 testu webusers 4734 Aug 19 13:08 HISTORY
-rw-r--r-- 1 testu webusers 2142 Aug 19 13:08 LICENSE
-rw-r--r-- 1 testu webusers 681 Aug 19 13:08 README
-rw-r--r-- 1 testu webusers 2883 Aug 19 23:24 index.php
