Can you provide some logs after sleep/resume? It sounds to me like your devices are reenumerating which could cause the problem you are seeing.
If the OS sees displays go away, the windows will snap back to the primary.
There have been quite a few issues with S3 causing VBUS pulses on some systems.
Our report tool can be found here:
http://www.displaylink.com/support/ticket.php?id=269