I've noted a huge difference in how my Brooks B17 feels between trainer and outside riding. Granted, there are only 22 miles on my new bike right now (wish it would stop raining), so that may be all that is going on.
On my bike I haven't even noticed the saddle riding outside. On the trainer" Girly bits get sore - even some numbness after the hour session on the trainer, and I find myself using unscientific methods to determine just where my sit-bones are hitting the saddle. On the trainer they seem mighty close to the rails.
Why such a big difference? Is it the trainer? Is it too early to worry about? Obviously the bike can't move under me on the trainer the way it does on the road...could this be it?