That's strange. Are you absolutely sure that you've seen this happen? I mean, later these gains show in the training reports as well?
Nothing was changed in this department though - You start training a spec. ability on your training and they no longer gain quality since all the training sips in to the SA and not the skills of the player.
Can you take some screencaps of your training sessions (when there are physical drills involved) when the next season starts? We gotta replicate this to know if it does happen, and then we can investigate further.