Trust me, you are not the only one who suffers eyestrain/headaches with IntelHD drivers. To make a long story short, about 2 years ago I purchased a late 2011 Mac mini (2nd generation i5, HD 3000 graphics) and for some reason, with DVI/Displayport, it kept giving me unusual eyestrain/headaches with both OS X and Windows 7 (Bootcamp), within 5-10 minutes of use (both at native 1920x1200 resolution and lower resolutions), on an LED-backlit monitor (100% hardware brightness to eliminate PWM but offset by low-contrast settings to lower effective illumination) whereas my previous PC (using a ATI 3870 DVI connection on the exact same monitor) caused absolutely no issues; I believe even an earlier (2005) Mac Mini caused no symptoms with a DVI connection to the same monitor.
However, when I connected the late 2011 Mac mini through an analog VGA cable, the symptoms disappeared with both Windows 7 and OS X. In fact, my main desktop computer is this 2011 Mac Mini running through a VGA cable at 1920x1200 and I have zero eyestrain.
More recently (since Dec 2013), I have tried several laptops with Intel i5 or i3 displays (HD4000, HD4400, or even Iris) and they all cause me eyestrain with Windows 7 or 8/8.1, regardless of the hardware brightness settings I use or the usage of software brightness/color-temperature control problems such as f.lux. I have tried a Lenovo Yoga 2 Pro, Dell Vaio Pro 13, and Haswell (late 2013) Macbook Pro Retina and they each caused similar symptoms, although the Vaio Pro 13 was the best of the bunch. More recently I resigned myself to a low-brightness (250-nits or lower) lower resolution laptop, so I bought a refurbished Acer S3 (i3, HD4000) running Windows 7. I noticed that if I use the Intel HD drivers a similar eyestrain/headache occurs, but if I use the "Standard VGA driver" in Windows 7, although I no longer have any control of gamma or software colors/brightness, the system is much more comfortable to use (the fact that peak brightness is 250 nits means that I don't really need to lower brightness from this level using software or hardware) and there is practically no eyestrain/headache. I also installed WinXP on this Acer S3 and while functionality is more limited (i.e. I haven't found drivers for the Wifi/Bluetooth), the Intel HD drivers do not appear to cause eyestrain in Windows XP. I also have an older Acer Aspire 1410 (2010-11), which also running Windows XP and IntelHD drivers, again is very comfortable to use.
Hence, I can only conclude that there is something in the Intel HD hardware drivers (HD3000, HD4000, HD4400 or Iris) that must be causing some sort of invisible flickering (temporal dithering??) or something that is causing eyestrain/headaches, when installed in Windows 7 or 8/8.1. I haven't tried a dedicated Nvidia or AMD/Radeon graphics system with Windows 7/8.x, but that could be the next step - although its' impossible to find high resolution (above 1366x768) modern lightweight laptops that don't rely on IntelHD graphics.