In our finished basement, there is a large crawl space. The floor is wood and is chest-high, the walls are sheet rock, and there's a small window at exactly outside ground level. When we open the sliding door, it smells inside...I think it's just a stuffy closed room smell, and my wife thinks its mold. On just a few parts of the wall, there are black mold-looking spots (which doesn't come out with Borax). A mold expert came and said that there might be a little mold, however he didn't seem concerned about it at all. This was last December, and nothing has changed, (we still store stuff in there which doesn't seem to smell) except that my wife seems still obsessed with doing 'something about that mold smell!' We can't always leave that little window open. Any other suggestions?
Maybe your wife is more susceptible to the "off gassing" of the active mold in the crawl space that you are. Mold off gasses the "musty" smell that most people smell it but not everyone does. There is likely to be mold behind the walls and under the floor where it cannot be easily seen. The black spots are likely to be mold and they can be cleaned with a commercial mold cleaner of you can mix 20% bleach with water and a surfactant like detergent (just a cap full for a gallon of water)
Try doing that it may help.
You can also rent an ozone generator for a tool rental place and follow the instructions that come with it. That will get rid of the smell for a temporary period of time. You can install an "air to air" heat exchanger in the space and change over the inside air as needed. You can also try raising the air temperature inside the crawl space to keep it dry. Mold needs moisture in order to grow. The drier it is, the less likely you are to have "active growing" mold.
Good luck, Daniel