I've had issues with Emodio software on our S3 devices as well. I used WMP 11 to transfer songs instead. Seems to recognize them every time while Emodio is hit or miss. When I have time I'm planning to look at using Media Monkey and possibly Songbird to manage songs for transfer to the S3. Only problem is I'll probably still have to use Emodio for video conversion and transfer.
What made me mad was the BestBuy website saying the device is Win2000 compatible and in reality it is not because it relies on the MTP driver from WMP 10 or WMP 11.