Every time I open my AT I get the hint that I have more spells to add. I pick a spell, save the character, open it up again and get to pick another spell. At one point I removed duplicate information in my Arcane Trickster CLASSBONUS line. I've saved and reopened once since then. Since I have 4 levels of sorcerer and 1 of arcane trickster should be an 5th level caster. The spells table show 6th level.
Sorcerer  0 1 2 3 4 5 6 7 8 9
Cast 0 8 6 4 0 0 0 0 0 0
Known 7 6 2 1 0 0 0 0 0 0
and that isn't right. Here is my class information
I've attached my character PCG file in case I didn't get this right.
ubuntu linux with sun java
Fixed for most saved characters.
However for characters which have been loaded and saved in 5.17.20 you will need to manually adjust the SAVE:BONUS entry on the CLASSABILITIESLEVEL line to remove the duplicates already added. Only one should be present in the case of the arcane trickster.