Auto Stack Freezes Program

I have a Dual 2.5Ghz G5 with 7GB ram and a Nvidia 6800 Ultra video card - well over the recommended specs in everyway. I am having issues with Autostack being slow (hours) and/or hanging the program. I have tried importing 6900 medium sized jpegs (shot with a Nikon D2h) from a folder containing a older projects I am doing, which seems like it should be with within the capablities of the program with the hardware I am using. I will then select auto stack, and can move the slider slightly to adjust the time interval before the program gives me the spinning beachball, which it will then spend hours trying to process or will then freeze the program indefinitely (I let it go for 11 hours once) at which time I have to force quit it.
I then tried it with a ancient project with jpegs from a Nikon Coolpix 950 which produced a averagew file size of less than a 1 Mb. I Auto-stacked 650 photos but still had the beach ball and it took about 10 minutes to complete- much longer than I expected with such small files.
I have not tried RAW files yet.
I hope somene has a answer on how I can possibly alleviate the problem, the auto stack is one of my favorite features so far when I can get it to work.
Even with this problem I can say this program is awesome. It's very power hungry, but truly unlike anything I have used and a excellent 1.0 effort.
Dual 2.5ghz G5   Mac OS X (10.4.3)  

Maybe this is why in the training DVD supplied with Aperture Apple recommends using the auto stack feature at the time of import from memory card or camera. There's a slider at the bottom of the import page which, if memory serves me correctly, does the auto stack command. This way you'll be stacking only say 100 raw images from a 1gb card and the numbers won't get too taxing.
Still, this should be a fairly simple fix for Apple to sort out so here's hoping they get on the case sharpish! I think the auto stack HUD is loading each individual image instead of just working with the attached data.
Power Mac G5 dual 2ghz Mac OS X (10.4.3) 2.5GB RAM, 9800 Pro graphics

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    agreement_rule = R
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    sales_territory_rule = R
    receipt_method_rule = R
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    argument12 => '',
    argument13 => '',
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    argument15 => '',
    argument16 => '',
    argument17 => '',
    argument18 => '',
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    argument21 => '',
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