It may be uploading two more files than the number of photos which you used, but not two more images. The two additional files are the Deep Zoom Collection file and the binary file containing the point cloud(s) and other synth metadata. If you watch the Photosynther folder in your Temp directory while a synth is being calculated you will see these two files be generated after the synther completes the "Reconstructing Scene" stage outside the 'images' folder.
A0000009 is a server error on Photosynth.net's end. I don't know of any steps to take to avoid it. I know I've gotten it a few times before, but the only thing I know to do is to retry your upload.
I'll try to upload a couple of things later tonight to see if I get the error as well.