After looking at my site with Safari, my web counter was wrong (visually and numerically)
Today I spent some time looking into this and found that the pipes (vertical bars) my ISP was generating for the IMG tag are not valid inside of a URI. A few hours later of dorking around with other scripts, I finally did the simple thing and tried replacing the pipes with ampersands.
Now, the counter is correct! Of course it is off by a few hundred, due to the improper counter, which I cannot change (the count files are kept out of my domain) but alas, the world is good again.