I'm also having this problem. However ...
Horses will gain traits on their own; for instance, if they play with the ball enough they will gain the Playful trait on their own, when they gallop sufficiently they will acquire the Fast trait, and if they surmount sufficient jumps (beginner or advanced) they will obtain the Agile trait.
What I cannot do is reinforce activities, such as brushing (obedient) or cleaning hooves (neat), to compel any horse to adopt those two traits. This was not the case prior to patch 1.333. To ensure this holds true, I tried repeatedly on 10 different horses in two different towns/families.
The least "cheatful" way of overcoming this problem is to go into Create a Sim and select traits like Genius, Obedient, and Brave for your horse; then, through the course of race and jump training, let your horse acquire the Fast and Agile traits naturally. That way, even with current glitch, your horse will have five positive traits and will sell for more, if and when you decided to put it up for sale at the equestian center.