After upgrading to the free version of 4.4.1 to support Mac OS X 10.9, "synchronize" no longer works when "upload" is selected as the synchronize-type in an SFTP connection; the checkboxes for all items are disabled and none are selected (see attachment sync_upload). Changing the synchronize-type to "mirror" enables the checkboxes (see attachment sync_mirror). In Preferences > Transfers > Timestamps, the "Preserve Modification Dates" checkboxes are both enabled.
The problem still occurs for me with version 4.4.3 (build 14140). See attachment sync_upload_443 and note the details for "index.html" show the local version has a newer timestamp than the remote file but its checkbox is disabled.