Aperture 2 simply refuses to import more than ~20k photos!

I just bought A2 for my 20" iMac w/4GB memory (2007, Oct, 10.5.4) and have about 44k photos to import. I went to import folders as projects (mostly because my "old" system was Adobe Photoshop Album, and I have about 400 folders as they were imported by that program - now Adobe Elements - and it seems it would take forever to import the photos individually folder by folder).
After importing about 150 folders (~20k photos) it stopped and came up with an error box saying some photos - listed them, about 30 photos - weren't imported (it singled out a particular folder with about 30 .nef files in it), no reason given...one option was to "locate in finder, hit that button, it did nothing...other option was to hit the OK button, and it disappeared.
So, I went back and selected a few other folders without this problem one in the list, but got the same message anyway, and now can't import squat, nada. I tried re-starting, etc.
Surely this software can handle this many folders/photos...is there another way to import my photos?
As my iMac drive is only 320 GB, I have all my photos on a 1TB Seagate Firewire 800 drive and it's backed up by a 1.5TB WD drive attached to my Airport as the time machine. I tried to import them selecting the option to leave them where they were. Now only half my library is in Aperture!
Help! I can't go back to Photoshop Elements!!

Thanks for the input, good suggestions. I don't have the tilde sign in the path anywhere. My naming convention has been; folder name generated by Adobe Photoshop Elements/Album, and my own, simple year month. Within that, is the name given by my Nikon D100 and D200.
I initially did about 15-20 folders at a time, around 3k - 5k images, and it worked up until that last one...now, I can't even generate a SINGLE photo into Aperture. And, when I browse through the import screen within Aperture, it sees the folders, but when you click on one folder, it shows no images in it, none. But they are visible in Leopard's Finder and are obviously there.
I am thinking there may be a bug, too. perhaps a re-install? And try again?

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