Flickr - "Houston, we have a problem." error happens with every upload?

I downloaded the direct uploader thing for Flickr and everytime I try to upload my 3,000 pictures it fails. I keep trying and it just adds the same photos and then fails and then I try again and it freezes up.

What gives? How can I get all 3,000 photos up, without any duplicates?
Update: I have Pro.
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