Just to let you know, as I was leveling up i did not level my companions until they were 9 levels below me as you get 3 levels from each tome that way (so basically trying to keep them even at 9 levels below you will end you up with well over 75 tomes at level 50, and you can survive just fine. Also you do not need crowns to level your companions.
<1% chance means that companion has less than 1 percent chance of joining, like a 0.9% chance is less than 1% chance.
I've also experienced this. With my Buccaneer, I don't favor Musketeer companions for him, so all of his Musketeer companions (except Bonnie, Rooster, and the Mustang Gaucho) are on the second page. During an important dungeon, his watermole slingman came into the battle, twice, and he's the very last companion on my Buccaneer's list.
This the best theory i have. All your companions with the exception of your first mate, their chances all add up to 100% so just think ofit as a giant spinning wheel everytime you enter a battle the dial spins and lands on a companion slot. Even with this it still doesn't make any sense, KI probably just does this to make us use your unwanted companions so we can better our strategies when it comes to situations we don't have our favored companions.
Don't forget that random numbers are random. While it is not probable for the companions at the end of your list to be in multiple battles, it is possible. The fact that you got that companion in the last battle has no bearing on whether it appears in the next battle or not.