The Atalasoft BarcodeReader can sometimes get "confused" by multiple barcodes which are a bit too close to each other... this can result in missed barcodes on a page even though the barcode images are completely valid and should have read.

Here are two sample methods (meant to be used together) to perform an iterative read:

/// <summary>
/// The DotImage barcode reading engine may get confused by multiple barcodes in too-close proximity
/// to each other... this method will use an iterative process to try and read what it can, then
/// hide the codes it found and re-read to see if more barcodes can be found...
///
/// It will continue looping until no new barcodes are found.
/// </summary>
/// <param name="image"></param>
/// <param name="options"></param>
/// <param name="useThresholding"></param>
/// <returns></returns>
private BarCode[] ReadAllBarcodesFromImage(AtalaImage image, ReadOpts options, bool useThresholding)
{
    // Doing this ensures we are not modifying the image object that was passed in
    AtalaImage imgCopy = (AtalaImage)image.Clone();
    List<BarCode> allCodes = new List<BarCode>();

    // the first pass uses an unaltered image so just do that first
    BarCode[] codes = PerformRead(imgCopy, options, useThresholding);

    // Now, we will set up the Canvas which we will "white out" found barcodes from the previous run
    Canvas c = new Canvas(imgCopy);

    // iterate the results, doing the whilteout.. then try re-reading to see if we get more results
    while (codes != null && codes.Length > 0)
    {
        foreach (var bc in codes)
        {
            // Ok, we have a barcode... add it to the return list
            allCodes.Add(bc);

            // this code will write out a white rectangle over the location of the found barcode in the image supplied...
            // that will allow the engine to have a new, fresh view of the page where the already found codes are not present
            c.DrawRectangle(bc.BoundingRect, new SolidFill(Color.White));
        }

        // once again, we do a read.. if we end up not finding results we're done
        // if we find any new barcodes, we'll repeat the process, adding barcodes to the already found ones
        codes = PerformRead(imgCopy, options, useThresholding);
    }

    // this is no longer needed, so clean up after ourselves
    imgCopy.Dispose();

    // finally, return the results as an array
    return allCodes.ToArray();

}

/// <summary>
/// We need this method because even though we're updating the image directly the engine needs a new, updated copy 
/// </summary>
/// <param name="image"></param>
/// <param name="options"></param>
/// <param name="useThresholding"></param>
/// <returns></returns>
private BarCode[] PerformRead(AtalaImage image, ReadOpts options, bool useThresholding)
{
    BarCode[] results = null;
    using (BarCodeReader reader = new BarCodeReader(image, useThresholding))
    {
        results = reader.ReadBars(options);
    }
    return results;
}

Original Article:
Q10422 - FIX: BarcodeReader Misses One or More Barcodes on an Image Containing Multiple Adjacent Barcodes