As part of the Companion Testing, I decided to use ABILITY:Animal Trick|NORMAL|Animal Training ~ blah
It now works, but the AbilityPool shows a Pool Count of '0' and Available of '-6'. The Correct Values should be '7' and '1'. However, Should I try to remove the Ability in question, it doesn't remove, but the Pools both update and correctly reflect the correct values.
This can be tested by creating a Level 1, Human or Halfling Cavalier. Add a Camel Companion. Switch to Companion, Look at the Class Abilities (Animal Tricks).
Bonuses from the companion mods were not being activated.