I used to have the same problem (data drive as a system drive). After days I've found solution:
1) Download and install Sysinternals Process Monitor Process Monitor
2) Start System properties - System protection (with button "Create").
3) Run Process Monitor and set Filter:
Process name is SystemPropertiesProtection.exe4) In System protection press button "Create" and make a restore point.
(SystemPropertiesProtection.exe is name of process, which creates restore points).
5) In process Monitor find every occurrence of your not system drive, eg. "D:\" (without quotes).
After these steps I could find the reason why Windows 7 thought that my data disk is system - I had two incorrect junk links from system drive to data disk. Windows followed these junk links and tried to find some Windows gadgets...
I corrected junk links (from system disk to system disk) and finally is my backup working.
Thanks Sysinternals for their small useful tools - only Process Monitor could reveal me why Windows recognized my data disk as system disk.