I wanted to close this thread out. I figured out the issue. My stream wasn't 
correctly converting the bytes to ints. It needed to shift the bits so that if 
the byte FF was encountered it wasn't returned as -1, but as 255. In fact, all 
negative bytes were probably causing issues. The fix was to change my read 
method to this:

    public int read() throws IOException {
        return (index < bytes.length) ? (bytes[index++] & 0xff) : -1;
    }

-bp



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