With Amazon you will want to win the buy box on as many of your items that you can. However you may not be aware that there is actually more that one Buy Box on each listing, and different sellers can hold these at the same time.
New/Used Buy Box:
You can see from the image below this particular item is showing both the new condition Buy Box, and used condition Buy Box. Although here you cannot see which seller holds the used Buy Box, you can see who holds the new Buy Box. So this item has both a new Buy Box, and a used Buy Box. Some items may not have a used Buy Box at all, and even some items may not have a new Buy Box.
Prime/Non-Prime Buy Box:
There can also be another Buy Box type which can cause confusion. There can be a prime Buy Box and Non-Prime Buy Box. How Amazon display this is if you have signed up for Amazon Prime you will see the Prime Buy Box, you cannot see the Non-Prime Buy Box. Same goes for if you do not have Amazon Prime, you will see the Non-Prime Buy Box, and will not be able to see the Prime Buy Box.
This could cause confusion in RepricerExpress for example if you have Amazon Prime, and hold the Non-Prime Buy Box. RepricerExpress will show that you hold the Buy Box, but when you check on Amazon you will only see the Prime Buy Box so you will see another seller holding the Buy Box.