Google Base has done this to me a couple of times, but I just retry and it usually works the 2nd or 3rd time.

I have always had one product that doesn't work though. Every time I upload, I get 949 out of 950 uploaded, or 1099 out of 1100 (always one missing)...... It has to be an error in the output file.

I scanned through the file but nothing obvious there and for the sake of one ellusive product, I wouldn't spend too much time on it.

As for you missing over half your products, have you tried splitting your feed file into two seperate feeds? Perhaps Google doesn't like the size of your file. That would be the first thing I'd try.