The Lowest FBA Price does not get retrieved if it’s not among the top lowest priced listings. Amazon takes the first 15 lowest priced listings for every condition category (New/Used/Collectible), and it groups them together in to buckets. If the Lowest FBA Price is not within the first 15 lowest priced listings for every condition category then it does not get retrieved and you cannot compete against it.
In other words, if the first 15 lowest priced sellers for each condition category are all Merchant-fulfilled then there won’t be a Lowest FBA Price for you to compete with.
This is a limitation imposed by Amazon and it impacts all 3rd party software, not just ours.
Note: You can see how many listings have been retrieved out of the total number at the bottom of the screen: