Here's what I have done with success for stubborn mold.
When you wash the saddle with vinegar (white vinegar, 50/50 with water), you have to have a bucket full of wash cloths and use a NEW wash cloth with EVERY wipe. You do NOT want to put mold back on the saddle by using the same washcloth on the whole saddle. Wipe down every available surface. Use a soft toothbrush or paintbrush to get th evinegar into cracks or crevices. Once the saddle has been totally wiped clean with vinegar, use a clean wet washcloth to wipe off any left over vinegar. Let the saddle totally dry in your house.
Then, take it outside in the DIRECT sunlight, preferably afternoon sun. Let it sit out there for a couple of hours, rotating the saddle if you need to, to make sure all sides of it are exposed to 45-60 minutes of direct sunlight.
If the saddle has a fleece underside, use Lysol and saturate the fleece lining, allowing it to dry in the sunlight. Use a dog or cat slicker brush to fluff up the fleece once it's dry.
Bring it back inside and give it another thorough vinegar treatment.
Then (likely the next day) clean the saddle with Castile soap. You can get it from most Wal-Marts or grocery stores. It's in the laundry isle. It has less oils in it than saddle soap or murphy's, and is gentle enough to use on leather. Clean it with a sponge, frequently washing out the sponge in clean water (don't just dip it back in the same bowel of water to re-wet it. Use a soft toothbrush to get into all of the nooks and cranies of the saddle.
Now, day 2, set it outside in the afternoon sun again, to get another good sun treatment. The sunlight KILLS fungus and bacterie relatively quickly, so sunlight is your friend when trying to get rid of stubborn mold.
Once it's totally dry, bring it back inside and condition it with a conditioner that contains a mold inhibitor, like Leather Therapy. Condition all available surfaces, with 2 or 3 coats.
When you store the saddle, leave a white towel draped over it. Swap out the towels regularly, bleaching them between uses.