This is in reply to my previous comment about trying out two ATI Radeon HD 4870 cards to see if it produced the same logout error as using multiple GT 120 cards.
Well, I bought two ATI Radeon HD 4870 cards, only to find out that the motherboard will only accept one because of the only two available 6-pin power cord attachments (the one card uses both). Anyway, I installed the card and can run two monitors off that one card perfectly. Previously I had experienced sluggishness and choppy graphics when trying to run two monitors off of one GT 120 card, and that option was not viable.
This temporarily will allow me to use dual monitors without any issues, and I can already tell that the card gives substantial better performance than the stock GT 120 that the early 2009 Mac Pro model came with even with two monitors running off it concurrently.
I have also tried hooking up one monitor to each of the new HD 4870 card and the old GT 120 card at the same time, and as dozens and dozens have reported, the logout issue persists.
For now, I can at least say that I am much happier than before, as I can truly use my previous setup of dual monitors off the one new HD 4870 card perfectly. Still a bandaid on the problem, but I can work as before until Apple finally decides to get on the ball and fixes this major OS issue.