I just found the same issue after upgrading to Ubuntu 9.10 and VirtualBox 3.x.
For some reason the package qemu-kvm got installed and that's what runs the kvm 
module.
Before I was using VirtualBox 2.2 (not the OSE version, but the personal use 
version from virtualbox.org) in Ubuntu 9.04. I don't know whether qemu was 
installed or not. I don't remember doing so and I'm sure I never used it, but 
it might be.

The Ubuntu upgrade disabled the third party repositories. I had added the 
VirtualBox one as, if I remember correctly, it was not available in the 
standard repositories before.
Then the installed VirtualBox 2.2 failed to start because it could not load 
some kernel module (didn't complain yet about KVM, but I don't remember the 
details), so I went to add the karmic repository from VirtualBox.org to 
Synaptic.
When going to mark the VB 3.0 package for installation, I saw that the OSE 
version was available, so I just removed the third party repository, updated 
the package list, and installed virtualbox-ose 3.0.8-dfsg-1ubuntu1.
That's when I got the error message described in the bug report.

So, I'm not sure what actually triggered the issue in my case: the
change of VirtualBox version, or the upgrade to Karmic.

What I've done is deinstall qemu-kvm (and qemu with it).

-- 
VirtualBox can't operate in VMX root mode.
https://bugs.launchpad.net/bugs/292588
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