I went to Ottavia, and tried running yum update. It was having dependancy issues with mjpegtools, which was a rpmforge provided package. In order to get it to update, I moved the rpmforge priority above (a lower number) that of epel ( epel -> 20 from 10, rpmforge -> 10 to 20). This resolved the problem and the updates proceeded (all 434 of them). yum update on Ottavia now reports nothing needs to be done.
I went to Rosalba and found rpmfusion repositories enabled. The only one of the 3 repositories in each file enabled was the first one.
I then added priority listing to all the repositories on Rosalba. I set CentOS-Base and related to priority=1. I set CentOS-Media.repo priority to 1 (although it is disabled - just to head off future problems). I set all epel related to priorities to 20. I set all rpmforge related priorities to 10. I set all rpmfusion related priorities to 30, and left the first repo in rpmfusion-free-updates and rpmfusion-nonfree-updates were enabled. All other rpmfusion testing repositories were disabled by me.
I then had to by hand downgrade expat to expat-1.95.8-8.3.el5_4.2.x86_64 (the rpmforge version). I also removed and reinstalled x264.x86_64. Lastly I removed and reinstalled lyx. yum update was then run and completed successfully.
I installed yum-priorities on Allegra and made all CentOS-Base repositories priority 1. I similarly made the still disabled CentOS-Media priority 1. I made all epel related repos priority 20. I made all lscsoft repos priority=50 (not sure why its on Allegra and none of the other ones). I made all rpmforge priorities 10. I then ran "yum update" which updated 416 packages.
So basically all the Centos control room machines are now using the following order for repositories:
CentOS-Base > rpmforge > epel > (rpmfusion - rosalba only) > lscsoft (allegra only)
I'm not sure if rpmfusion and lscsoft are necessary, but I've left them for now. This should mean "yum update" will have far fewer problems in the future.