The type of FireWire connection in use (motherboard or expansion card) is not going to make your interface "noisy". Incorrect FireWire drivers or settings could cause pops and drop-outs in the audio, but not noise. Persevere with this FireWire connnection, as changing to connecting through a PCIe card is not going to solve anything unless the drivers for the PCIe card happen to be more compatible with V64.
If you bought this PC as recently as you say, did it not come with the option of a Widows7 upgrade?
Maybe what others can learn from this is: do your homework before purchase!