All you need to do is play once with your Ballplayer in a DD game. I am a starting pitcher for the Tigers currently, and i just do an offline game and I pitch one inning. Then I quit the game and go to RTTS and I have no issues progressing on my program.
If you are a position player, all you need to do is have one full AB. After that you can quit.
You will need to do this every time you load up the game to make sure you progress properly. Obviously it's still annoying, but it is a temporary fix until SDS provides us with a proper fix.