I've built systems using motherboards made by Asus, Abit, MSI and DFI and have not really had problems with any of them.
The only thing I noticed was that the system I built with the DFI board seemed slightly more unstable than the others possibly because DFI mainly make boards geared towards getting as much performance as possible from the components, but the problem was solved by flashing the motherboard to the latest BIOS.
Generally so long as your motherboard has the latest BIOS and fairly recent drivers installed in windows you should be fine.
Hope this helps