From my limited experience there are 3 motherboard features that will upset the CNC apple cart:

1) Power saving
2) On board graphics
3) Latency

1) Power saving features. Turn them OFF, all of them. You can experiment with them later if you wish but for now they go.

2) It is totally possible to make at least some on board graphics implementations work with Mach/LinuxCNC but the quick and easy answer is DO NOT use on board graphics. Plug in a dedicated graphics card, anything made in the last 10 years will probably be better than any on board solution more than 3 years old. This is especially relevant to portables or MBs designed for low power consumption applications.

3) Latency. What's that then?
In this case it is the time between the SW saying something needs to done and the actual signals to accomplish the task leaving the PC. Not quite that simple but close enough for now. Latency is inherent to the chipset though the SW and OS also play their part.

What are your latency values? LinuxCNC has a test that returns some big number, Mach has some similar test but it's so long since I used it I forget the what and where.

The operating system also plays a big role when it comes to running CNC and doing other stuff at the same time (and Windows is always doing other stuff). When I set up my first MB, a Jetway J7F2 http://www.jetwaycomputer.com/J7F2.html , I could get Mach working fine, until that is I moved the mouse! No kidding, move mouse = missed steps. Under LinuxCNC that problem went away and I was able to file share and run remote access. In general and especially with underpowered HW, LinuxCNC yields much more predictable and consistent results, the copy of Linux that comes with LinuxCNC is specially built for real time control, out the box Windows is not. Even so, the Jetway board very soon went away.

So, latency?