What is wrong with my setup? FCP 6 slow as snail.

I have been going nuts trying to troubleshoot what's going on with my system for a while without understanding what's wrong.
I am editing some HDV footage and all is well the first hour of editing. After that the system becomes so slow that clicking anywhere in the timeline takes the slider 10 to 30 seconds to react, not to mention playback just halts. I do not have the spinning ball, I can move the mouse but I cannot do anything with it (nor acess dock or finder when this happens). The system goes so slow that it basically is impossible to continue working on it. Not even a full reboot of the Imac gets the speed up.
About a month ago I bought myself an Imac 2.8 extreme, 3 gigs Ram and 500 gb internal disc, to be able to edit HDV footage (as my old Imac g5 was getting too slow for this task). It's not a macpro but it should be fine. I am working off an external 640 firewire 800 disc (newly formatted, 500 go free). I know HDV isn't the best codec to edit in so I even tried reencoding the media to apples intermediate codec but had same result with system slowing down.
I am getting worried that this may be an issue caused by the new iMac's graphicscard (as many new iMacusers are having problems with freezes) but apart from this I have never had a single real freeze of the system.
if you have any idea what might be going on I really appreciate any, ANY, feedback.

Be sure you're using the latest drivers for your Decklink...
If you didn't perform a totally clean install of the studio 2 when you got it, that might help. It's always been my habit to rebuild my startup disk any time a new OS comes out (i.e. Panther to Tiger) and when a new studio is released... I just have a very stable system as are the ones I watch after. I'm totally convinced this needs to be done periodically. At the school I teach at part time, there are about 65 FCP bays. They do this totally clean install every single semester. I'm convinced that this is the reason they are so stable in general, even being used by many user accounts etc...and by novice users to boot.
Also keep in mind that as drives get fuller, they get slower... so need to keep at least 10% free... they actually start slowing down at 70% capacity. As a side note, CalDigit's new HD PRO unit is stripped in such a manner that it doesn't slow down as it fills up... Apparently they stripe it so that every other drive is using the fastest part of the platters and the others start by using the slowest part of the platters or some such...
Jerry

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