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I've gotten the Error 99 in three separate cases:
Canon 10D with Sigma 300mm f/2.8 lens. Lens worked properly on D30 camera, it would happen when trying to set the aperture to anything other than f/2.8. Sigma was re-chipping the lenses for 10D compatibility, so this was due to a communication error to the lens.
Canon 10D with slow memory card. The card was not fast enough to write data as quickly as the camera needed, so it would freeze up with an Error 99.
Canon 40D with Canon 24-70 f/2.8 L lens. The contacts on the lens were dirty. Cleaned the contacts, problem went away.
Basically all that this proves is that Error 99 is a generic "things did not go as planned when communicating with an accessory" error. Given that you state it happens with no lens attached, I'd check both the internal backup battery as well as the memory card. For that matter, some li-ion battery packs have chips in them as well to validate that the battery is in fact OEM. Are you using a genuine Canon battery?
Regards,
Eric
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