While the boards may have the same features and chipsets, they'll have different components.
The VRM's, the audio codec, heat-sinks, the PCB layering etc. If your manufacturer tries to cut costs by using lower quality components, you'll notice it in the long run.
Also, low cost manufacturers won't have the budget to update the BIO's and iron out compatibility issues.
But if you're never going to upgrade, keep your computer in a cool, clean place and use it for just basic office stuff, then I don't think it matters if you go for a tried and tested board or one from a lesser known player.