Ap 3.2.1 update majorly messed up

Auto software update prompted me that there was a fix for Aperture 3. It would fix the orientation issue with cropping. Yes, I was happy about that.
Dowloaded, installed, and began using Aperture.
Oh my, Apple you got some work to do. All the brushes I've used so far (repair, cloning, etc) are really badly messed up now. The update somehow blew them out of the water.
Example: cloning. I choose my source, move the circular pointer over the area to receive the clone, and the circle starts flashing and blinking. That in and of itself isn't the biggest issue. Usually the source material is displayed in the circle. Not anymore. What I see is a square box underneath the circle that is displaying, ummm, I'm not sure what it is displaying, but it isn't the source material.
Not only is there some kind of box under the circle, but there is a flashing effect of the source material that is attempting to overlay onto the area to show the cloned material.
Now, if I ignore all that and just "do it," it will turn out ultimately with the correct application.
The problem is that there is so much "interference" during the process of trying to figure out where the cloned material will be placed that it is rather difficult now to use clone.
Help Apple?
-Robert

forgot one Major detail. this is happening in Photoshop CS4 extended.
I opened the pic from Ap3 before I made the update. Everything worked fine between Ap3 and CS4.
Shut everything down, installed the update.
Restarted.
Opened programs. Opened the pic from Ap3 into CS4.
CS4's brushes are now the ones messed up as described above. They were working fine up until I made the update. Not sure how the update to Aperture would impact CS4, but it sure did.
-Robert

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