According to the Soekris "Downloads" page, there is a new version of the ComBIOS for the Net5501;
http://www.soekris.com/downloads.htm
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Currently available BIOS Files for net5501:
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b5501_132i.bin net5501 BIOS release version 1.32i
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http://www.soekris.com/Software/changelog.txt
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"comBIOS vers 1.32i
* fixed PCI config byte/word write handling (IDE DMA enable)"
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I have yet to try this new ComBIOS version with a harddrive.