It's now out of Beta form and the issue still exists, I have 2 stalls, discarded the horse that was in first stall and now all I get is the scrawny nag in online story missions. Gonna try to buy a cheap horse to put in that stall to see if that forces my main horse into story missions, if that doesn't work ill do what another suggested and sell the cheapo horsey - I'll let y'all know if either works