SD cards generally have very slow write speeds (as opposed to read speeds) and USB transfers don't always have the highest bandwidth. 12 hours to transfer about 2/3 of a TB is about 15MB/sec. SDHC cards are generally rated to have a minimum 10MB/sec write speed, so it sounds like you're actually beating the specifications on your card by hitting 15MB/sec. That rate of transfer seems as expected with your hardware, and if anything might be faster than expected.
If you want to speed that up, you'll want to look for an SD card with a faster rated write speed (often sd cards made for high def video have higher write speeds), although most SD cards aren't that much faster. The very fastest ones can be quite expensive and have write speeds that are four or five times faster (I think the highest rated I've seen have been a 60MB/sec rated write speed), so in the best case you'd be spending more to shave down the transfer to two or three hours at best (assuming there isn't another bandwidth bottleneck somewhere else like the USB connection, etc.)
As for duplicates, they're items that appear multiple times in the playlist you're trying to sync, so JRiver won't sync them twice or more. JRiver writes files to a path on the device using the rules you configured in the handheld options, and if the multiple files would be written to the same path JRiver identifies them as a duplicate (and I think JRiver identifies duplicates in some other cases too). If you're confident that the files you're trying to sync aren't duplicated elsewhere in the sync, post more details about the files you're trying to sync.
