Ok, I've found the culprits that rendered the system unusable if you did a system wide upgrade and I have them removed.
Unfortunately, I don't have a solution for anyone effected other than a reinstall.
Some good came out of this, however, as I discovered some good techniques for testing new packages and there behaviour during a system wide upgrade.
I still don't encourage users to "Mark All Upgrades" and Execute, but as I work this testing technique into my regular maintainence routine, I think it will become a safer move to make in the future.
I will be working somethings back in over the next few days, that I took out trying to find the problem. So if you find something missing, (like xfce4-4.10) it will be back in a few days.