As an unsuccessful internet marketer for a few projects, I can vouch for your story. Sometimes the various statistical packages just don't add up very well. My hypothesis is that these packages can be overwhelmed with data that they just can't record everything.
But sometimes there are sinister motivations. I was advertising one of my inventions with both Google and Yahoo ads. I also had statistical code embedded that section of my website. It was recording traffic from Yahoo. But I had also signed up for Google Analytics. It recorded roughly the same numbers from Google Adsense and Google Analytics. Because they were not exact, one or both of them was not recording a few things. But Google Analytics said there were ZERO visitors from Yahoo, but did mention other sources. i would call that a deliberate attempt to dissuade me from using Yahoo.
My stats program is independent of these two. It was recording about 70% of what Google said it was sending to my website. But I get a feeling that stats package does not record every visitors (I'm still using it).
My experience is that there will be discrepancies that cannot be easily explained. It's best just use these programs on a qualitative basis.
The only statistic that really matters is if more money comes in than goes out.