Because you are smelling microbial growth on damp wood, and because roughly half the air in your ground floor rooms came up from the crawl space first.
The Stack Effect
Warm air rises and leaves a house through the upper levels, and something has to replace it. What replaces it is drawn in from the lowest openings available — which, in a house over a vented crawl space, means the crawl space.
Estimates vary, but a substantial share of the air you breathe on the ground floor has passed through the space underneath. If that space smells, the house smells, and no amount of cleaning upstairs will change it.
That is also why crawl space damp is not purely a structural concern. It is an indoor air quality one.
What Produces the Smell
Mold and mildew growing on joists, subfloor and insulation. They need moisture above roughly twenty percent wood moisture content to become active, and in a vented Tennessee Valley crawl space they get it every summer.
Wet, decomposing organic material — old insulation, cardboard, leaves that have blown in through vents.
Occasionally something worse: a dead animal, a sewer leak, or standing water that has gone stagnant. Those smell different and they are worth ruling out.
Why It Is Worse in Summer
Because summer is when the mechanism runs hardest. Outside dew points in the low seventies, framing at sixty-five, vents open, condensation forming daily. Growth accelerates, and the stack effect is stronger when the house is air conditioned and the outside air is hot.
A crawl space smell that appears in June and fades in October is telling you exactly what is wrong.
What Does Not Fix It
Air freshener. Bleach sprayed over live growth without removing it. Opening the vents wider, which is the instinctive response and precisely the wrong one — more vented summer air means more condensation, not less.
What Does
Stop the moisture. Remove the contaminated material, clean the framing properly, then seal the space, line the floor and control the humidity. Held below about fifty-five percent relative humidity, wood stays under the decay threshold and there is nothing for growth to live on.
The smell goes because the cause goes.