I had the same problem when trying to 'batch copy' all 20,000+ photos from a USB 3.0 external flash drive (1.5 Tb Western Digital) to the Time Capsule so I can start to use the WD drive to hold the Time Machine stuff, and the Time Capsule (ie router + HDD) to hold the family photos so my wife can see them on her computer with only one hop in the network.
When I pulled the whole "Our Pictures" folder over, it started to copy, but before it got to where it could estimate the amount of time it would take, I thought it might have stalled and clicked the little 'x' cancelling the job.
I then did a test-drive / proof of concept move of one tiny folder that has one tiny photo in it, and it moved over in a split second.
Then I started moving the folders one or two at a time, and they went just fine.
It seems to be a mis-match between what the computer thinks is reasonable (I'll spool up for the next hour, then work like a dog for 8 or 10 hours, then let you know when I've finished!) and what I think is reasonable (Tell me how far along you are within a few seconds or I'm going to question your ability to even do this job).
I'll bet if I left it sitting there long enough it would have finished the 'batch.' I am going to pay extra in time, in that there will be 'downtime' this way - the minutes it is sitting there with nothing to do between me moving a smaller package into the queue.
