I was on version 6.2.6.0, just upgraded to 6.2.6.1 which has improved the situation, but not by much.
I can now download just the first season of any given series, but beyond that the StreamFab analysis can’t see any more seasons.
My region is Prime India, which recently upgraded its interface, so that might have something to do with it.
Example: I just tried to download Jack Ryan the series, which has 4 seasons. When the analysis page completed, it showed just 8 episodes for season 1.
I tried the same for other shows, and it comes up with just the first season of each.
The only thing that works is to copy the URL for subsequent seasons and paste it into StreamFab, which I personally don’t mind doing as this is how I did things before to ensure the right bitrates for the given season.