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I would put the 20GB on the motherboard IDE 1 channel and then use the WD Data Lifeguard tools to Write Zeros (aka Low Level Format) to the 20GB.
Then use FDISK to delete any existing partitions, create an extended partition with a logical partition, and then format it.
Then put the 20GB back on the Controller card and see if Windows will assign a drive letter to it.
As RJ said, jumper both HDs to CS on an ATA66/100 cable.
If you're still having problems, then try putting the 20GB on the Secondary Controller card channel. Sometimes two different brands of HDs don't mix well on the same channel.
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