You should try rsync to monitor your transfer speed. For example:
rsync -PSauv sourcedir/* destdir/
If you actually see a drop in transfer speed, as opposed to files that are just big, then you need to look at a few other things.
If your disk is I/O-bound, you will have problems. You often see this
when writing heavily to a flash drive or an external USB device.
Test both your disks with
hdparm -Tt <device> to see if one is
dramatically slower than it should be, or dramatically slower than
the other device which can lead to I/O issues.
Check your dmesg output and your SMART status to make sure you
don't have any obvious disk errors. You might also consider
badblocks -n if you suspect disk errors on a non-SMART drive.
There are lots of reasons why a disk can thrash or perform sub-optimally, but until you can measure the problem, you won't know what the problem is. :)