Okay, since I recently had this problem, I will tell you the only garaunteed way to fix it.
Firstly, to explain why it happens, you must understand that newer drives run with a low level software called a drive overlay. This software, even if not needed, will install itself on any drive you connect to your system. This was originally intended to bypass the 130 or so gb barrier on XP before SP1, and even more heinous, the hardware limitations in BIOSes on older mobos. I don't recall the exact volume of the limit. Regardless, it's been around for a long time, and can even end up on small drives. I've had it install on a 20GB drive. Most modern mobos do not need it. Google EZ Drive and you will see that I speak the truth.
The point is, the Drive Overlay will install itself on any drive and SUPERSEED the MBR, or Master Boot Record.
Your data is not lost, windows just can't see it becuse the drive overlay stores the MBR for logical disk 1 and higher on disk 0's MBR. This is a retarded setup, but it's how it runs. The long and the short of it is that when you dump drive 0, you lose drive 1 and up.
The cure? This ones a toughy, and you are going to have to buy a program to fix it. MAKE ABSOLUTELY CERTAIN THAT YOU DO NOT RUN DEFRAG, FORMAT, REPARTITION OR DO ANYTHING ELSE TO THE BLANK DISK OR YOU WILL LOSE YOUR DATA FOREVER.
This is the site where you can get the program:
http://www.ptdd.com/
From the operations menu, choose rebuild partition and let it run. After some time, let it rebuild the MBR on that same disk. Move on to the next disk and repeat from the begining, you will get your data back garaunteed. Remember, if you do anything that writes to either of those disks, you will lose your data permanently.