This can happen under two conditions:

1. You haven't assigned your ads to their respective books in Author Helper Suite. 

2. You have more than 300 results in your AMS ads report. As of this writing, Amazon only displays 300 of your ads results on their reports page. If you have 301 or more results/rows in your file then you'll need to download page 1 from AMS, skip to page 2 and download those results as a separate file, skip to page 3, etc. You can upload each of those files without overwriting anything.