That sounds a little strange but I am not running A3 on anything that old - I can tell you that on my old MacPro (1st Gen) that the upgrade to the NViDIA graphics with 512Meg VRAM was critical to Aperture performance - the stock graphics made aperture really really really SLOW on large files.
I had the same experience. It seems that Aperture does not manage the accumulative brush strokes well. Even if you create a new 'version', the brush history doesn't go away and piles up in your RAM and somehow keep your CPU busy. I don't know if it helps but I found a workaround (not a solution) just to finish my retouching. Each time the brush became slow, I right-clicked and chose an external editor (I have Pixelmator as external) which promptly opens the file in its own window. Do a token editing just to create a new file, and save. The new file will then be saved as a new 'version' of the picture in Aperture, without all those brush history. You can then use the brush for a limited time with acceptable speed until it slows down again. At which point I repeated the same scheme.
The quality of the brush is really good. But it just shouldn't behave that way. No amount of RAM can cope with this. I have 16GB!
I had the same problem: after a heavy retouching session, suddenly my mbp 2.4, OS10.5.9, 4G Ram, started giving me the beach ball treatment. Research here indicated I was to empty ALL my cache files (I did), and that if the problem still existed it must be in my head as Aperture certainly seemed to be speedy for many many similar users. I would restart machine, close out other programs, but immediately I would get the "processing" indication in the lower portion of my image as soon as I opened it up.
Finally I decided to quit working on that image, but noticed that Aperture still showed "processing" no matter what image I worked on, and when I clicked on the "processing" icon, it indicated it was still working on the closed image.
So in desperation I deleted the file from my aperture library.
I haven't had the problem recur since.