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You probably have fakeraid signatures on the disks. Since Ubuntu 9.10 has fakeraid support by default, your fakeraids will be discovered and activated unless you use the "nodmraid" boot option.
The fake raid is on the disks, not on the motherboard. Linux/dmraid can not see if you have disabled the fakeraid support in the BIOS, but it sees the fakeraid signatures on the disks. If your BIOS does not have an option to delete the fakeraid configuration from the disks, use dmraid -E.