The new card just arrived, and I was a bit surprised by the fact that it is only 3" long, but that turns out to be a plus in my case, because the motherboard has 1 PCIe x1 slot at the top that nothing else would fit in, and it frees up a x16 slot the old card was using for something else.
I wasted no time installing it and voila!, no problem booting with the external drives turned on. The BIOS recognizes both drives and Windows did install some kind of driver for it, but I have no idea what, because the Storage Controllers section no longer appears in the Device Manager.
Oddly, I just started having problems with my HTPC, because it delayed about a minute reaching the Silicon Image 3132 card there, but it isn't a raid controller...