First and foremost, multiple monitors on all platforms (Windows and Mac) have to be set up as extended desktop...NOT mirrored or duplicate mode in order to profile.  Users will likely encounter a variety of errors attempting to profile multiple displays in mirrored or duplicate mode.  

Some Windows operating system are not able to set an individual ICC monitor profile for each of your dual monitors.  This is something that is handled by the operating system and can be true for Windows XP, Vista, Win 7, and Win 8.  There were very few graphics cards capable of applying individual profiles to dual monitors in Windows XP.  Support for dual display profiling became more common in Windows Vista and it has become much more common in Windows 7, Windows 8, and Windows 10.
  
To calibrate and profile dual monitors on Windows based system, your video card (driver) should provide the following features:

- Support for individual Video LUTs (lookup tables) for both monitors (support of two graphic chips)
- Support for handling individual ICC profiles for both monitors
- Dual monitors will need to be physically connected to individual ports on a single graphics card setup...no splitters or switches!

X-Rite's Technical Support and Software Development teams has done extensive research in the past using dual displays and the use of ICC profiles in these environments.  The most ideal way was to run a dual display setup from one operating system is to have the ICC profiles applied from 2 separate video cards.  This truly is the best way to ensure that the profiles are both generated and being applied correctly as so many cards do not allow the option to utilize separate LUTs from one card. Since Windows 7 was released, dual displays connected to a single video card will almost always support separtate LUTs. If you are creating and using 2 profiles on one card and are having issues with color, contrast, brightness or others, you may want to disconnect the secondary monitor and then try reprofiling the primary display to verify the accuracy.  Researching the video card through the manufacturer is also a great place to start to verify what the specifications of your particular card can handle.