The rpmfusion repo is NOT part of the standard VortexBox installation, and never has been. You must have installed some non-standard packages that caused the rpmfusion repo to be installed on your VB.
Andrew is correct; you can't have both rpmfusion and atrpms repos on a VB.
I suggest removing the rpmfusion repo if you want your VB to work as it should.
on a properly functioning VB 2.0 / F16 system.
repo id repo name
atrpms Fedora 16 – i386 – ATrpms
fedora Fedora 16 – i386
updates Fedora 16 – i386 – Updates
vortexbox Packages for VortexBox
You can try to get rid of the rpmfusion repo by
As long as you have both atrpms and rpmfusion repos active, you will run into all sorts of dependency issues when you try to upgrade your VB, as you have seen.
yum erase rpmfusion*
Once you have removed the rpmfusion repo, and have only the repos listed above, try upgrading your VB once again by
If this works as it should, it should install the latest kernel (3.1.5-6). Then when you reboot, this kernel should become active.
yum clean all; yum update
But you may find that you have a number of rpmfusion packages still on your VB that are causing problems. It may be possible to clear them out one by one, but I'm not sure how to do that. There should be NO packages on your VB from the rpmfusion repo. All A/V packages should be from the atrpms repo.
If you can't figure out how to remove all the rpmfusion packages and replace them with their atrpms equivalents, you may find it simpler to do a fresh install of the VB 2.0 ISO.
Otherwise your VB is going to be hopelessly messed up, and you will find that updates aren't going to work.