n7, interesting! do you happen to know the controller you used? Modern motherboards use additional controllers on PCI-express x1 bus, but if yours was on the PCI bus that would explain it being a lot slower.
When comparing the RAID drivers of JMicron/Promise/Silicon Image/AMD/nVidia they all fall to dust when compared to the Intel drivers; the only reasonably decent software RAID that exists for Windows. But if you do not use their drivers, you should be fine. I used JMicron JMB363 in my FreeBSD server (3x PCIe x1 cards each with 2 ports) and got very good speeds from them and quite low latency; though still a little higher than the chipset-powered controller which always should have the lowest latency, as its closest to your CPU. Note that if you connect a controller to PCI-express x16 ports, you may be connected directly to the northbridge, which may be the same latency of the onboard ports.
This latency is important when dealing with SSD random IOps, but not so much for sequential transfers.