I'm not sure why it's doing that, but you should be able to fix it... I hope.
Insert a drive
Open Computer Management
Go to Disk Management
Right Click on the Disk Currently Inserted > Change Drive Letter & Paths
Give the drive the first permanent letter (i.E. E, F, G, etc)
Now remove that drive and do the same w/ # 2.
If your drives are recognized properly by the computer, you should be able to hot swap them now and have them keep the same drive letter.
For example, I have 9 drives/partitions in my computer and they were completely jumbled. Then I changed the drives letters around and:
Oh yeah, when you disconnect your drive for another, make sure you disconnect via the safely disconnect box first in computer, then power down the usb dock, then pull out the hdd.