Usually, when you flash the bios you have to restore system defaults, then put your settings back. If you don't do this you can some very strange results.
I know you've looked at the bios settings, but did you restore defaults first?
Where did you get your copy of the bios?
If there's any doubt, download the latest (P19)
here
You should also look at the release notes, from version P18 onwards there's an option to disable the USB ports completely. It isn't clear where it is, but make sure that hasn't been selected by default. It isn't mentioned in the manual because the manual hasn't been updated since 2003. The manual says any changes to the bios will be reflected in updates to the technical specification, but guess what, that hasn't been updated either. Good old Intel.
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