This is not an issue with SyncToy but a security feature of the excellent trueCrypt. Even though you have updated the trueCrypt container file with new content, TrueCrypt has not updated the date time of the file to "pretend" the file has not been touched and thus make it harder to detect.
This behaviour is configurable in TrueCrypt: Menu: Settings / Preference - Just uncheck the option "Preserve timestamp of file containers".
Re-mount your container, update the content, unmount and Sync. It should work fine.
PS: TrueCrypt containers do not change in size.