I too have problems with synchronisation, synchronising files from a local Win7 machine to a remote Unix machine, using SFTP.
Under Winscp 4.2.7, "synchronise" works OK.
Under Winscp 4.2.8, "synchronise" identifies files with a DST difference as being different and wants to copy them; I let it copy them but the next synchronise STILL identifies those (now re-copied) files as being different.
I have reverted back to Winscp 4.2.7 and the synchronise works again - so it really is due to a difference between 4.2.7 and 4.2.8 - possibly bugfix 564.
Like the previous poster, I will try sending you an e-mail.
I am using the GUI "Synchronise local directory with remote directory (Ctrl+S) command.
Server/Protocol Information:
Session protocol = SSH-2
SSH implementation = OpenSSH_3.8.1p1 FreeBSD-20040419
Encryption algorithm = aes
Compression = No
File transfer protocol = SFTP-3
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Server host key fingerprint
ssh-dss 1024 07:a3:5e:ce:9a:19:fd:7d:70:eb:59:59:a2:26:69:1c
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Can change permissions = Yes
Can change owner/group = Yes
Can execute arbitrary command = No
Can create symlink/hardlink = Yes/No
Can lookup user groups = No
Can duplicate remote files = No
Can check available space = No
Can calculate file checksum = No
Native text (ASCII) mode transfers = No
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Additional information
The server does not support any SFTP extension.