Don't run the installer. Download the .zip file, extract it, and update the driver from the device manager.
http://lifeisabug.com/installing-latest-intel-hd-graphics-driver-microsoft-surface-pro-pro-2-pro-3/
You can actually run the exe file after you unzip it but you have to delete the SP3 drivers first. The benefit of doing it this way is that you get the Intel HD Display Graphics Control Panel program which I find to be very useful.
To do this:
1. Download the most recent
zip file of the 64 bit Intel drivers for your Surface (ie HD5000 for the i7) from the Intel Download Center
2. Extract it to a location that you will remember but don't install it yet. If you try to install it now you will receive thWhene error message
3. Open Device Manager and double click Display Adaptors
4. Double Click on the only driver that is listed
5. Select the Dr.iver tab at the top menu
6. Select Uninstall and the Confirm Device Uninstall window will pop up
7. Check the box for delete this driver software for this device
8. Restart the computer and login as normal
9. Go to the folder where you extracted the Intel display drivers and double click setup.exe and follow the instructions and the new drivers are installed. (Can't remember if it asks you to reboot or not.)
10. After the installation finishes open the Intel HD Display Control Panel, which should now be on your desktop if you selected this option during the install, and select Display and then select Color Settings to adjust your contrast and brightness settings. You can use your favourite black level and white level patterns to adjust these values.
11. Shortly after you have installed the new drivers Windows will advise you that there are is a new Hardware Update. Make note of that specific update because you don't want to install it in future updates. Don't install it and uncheck that specific update before installing future updates. It is important that you do not have automatic updates as your update choice. I selected download but let me know before installing.
12. Unfortunately this process has to be repeated when Microsoft includes new display drivers if you want to use the Intel Download Center ones. I check the HD5000 driver version after all major updates to see which version has been installed.