I had something like that happening way back, when testing the later 2.3 kernels and I think for a little while into 2.4.

Someone told me it was caused by the video driver hanging on to the PCI bus, and not allowing other devices to access it.

In my case the beeps would persist until I clicked a background window in my X session, to activate it.

I don't know if your problem is related but this would be a possibly helpful clue to investigate.

Mike
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Michael D. Crawford
GoingWare Inc. - Expert Software Development and Consulting
http://www.goingware.com
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  Tilting at Windmills for a Better Tomorrow.

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