Recently I have been copying a lot of digital photos between my hard drive and a variety of USB sticks and an external USB drive using synchronise. I noticed that the first pass does not always copy everything. There is no obvious pattern. Most times, all the files are synchronised first time but not always. Typically, the number of residual files is very small relative to the original number of eligible files. For example, I just copied around 200 images to an external HD and 4 of them were left behind after the first sync. I'll keep an eye on this to see if it can be reproduced.
Regards, AB