Mark,
Without images to process, it is difficult to see where the information is changing, but from the sounds of it, you are seeing information you thought was lost being saved in your report. If this is the case, you are most likely not saving the image buffer that you think you are, or there is a race condition where it is being saved before its processed. I know this sounds basic, but insert Windraw windows in your program so you can see you image as it is processed. It helps to use the Vision IMAQ Copy (White vi) so you can see the image at each stage, and it does not change its display as you proceed though the program. This will help so you can see exactly what particles are being sent to the file.
Best Regards,
Chris D