Warm air will hold more moisture than air that's not so warm. In other words, if the air temperature gets warmer as you more your gauge closer to the ceiling, you can be assured that the warmer the air gets, the more moisture it contains. Hence, the higher levels as you get closer to the ceiling.
40% in the crawl is very good especially being vented and having a dirt floor. 40% in the living space is good too. I wouldn't go over 45% if you had to push it. And it sounds like your attic is well ventilated.
What all this DOES sound like is your house is tight, up at the top. Do you have a dehumidifier running in the room where you have the moisture problem? Do you have on on your HVAC system? To control the humidity, you need both a humidifier (to add moisture when it's dry), and a dehumidifier (to remove the moisture.)
ANother thing, do you have return ducts in these rooms? In my home, there's one return duct in the hallway for a 4 bedroom, 2 bath, 2 story colonial. None of the bedrooms or bathrooms have one. This duct, as well as the duct on the 1st floor, are 30" wide. (We have a 12" duct in the Family Room whic was added as an addition to the house some 20 years ago ...) So, what I'm saying is 1) you need return ducts (that aren't obstructed), and 2) they don't have to be in every room. They just have to be 'well placed'.)
I'm not sure, exactly, what you're trying to accomplish here but if it's a balance with the humidity, I believe I've shed some light on it. You may need to consult an HVAC contractor for more particulars. They'd be familiar with 'what works' in your area, plus, they can see what you're talking about. :)