With Intel HD 4000 series we had experienced quite a few problems running Windows and Linux. This is due mostly with the drivers.
For example, on Windows you can run 3x 1080p displays but it will run on SST instead of MST. On the HD 5000 series we do not encounter the problem.
Another way to resolve your problem is to use USB Graphics, we have several models for USB 3.0. You can find this here