In general, if the lot you have or the town you live in has a high water table, 'space' below ground level is not constructed, usually, due to building codes preventing it. Therefore, I would say that by having a crawl space in your house, you don't have a high water table. If you did, I can't imagine the builder getting by an inspection w/o taking measures to migitage water in the space to begin with. So, I'm gonna go out on a limb and assume you don't have a high water table.
Assuming this ..., the next possible source of water is the result of inadequate drainage outside the home. The land needs to slope at least 1/4" per foot AWAY from the foundation all the way around the house. If the grading is not proper, this is a starting point to get fixed. Another source of water may be improper, or lack thereof, of gutters and downspouts. Make sure your downspouts have extensions of about 3' away from the house towards the downhill. If they're dumping water at the base of the outside wall, you run the risk of water getting in the crawl space. Also, check that the gutters are properly installed. They, too, need at least 1/4" per foot of angle to drain water. They shouldn't be HIGH on the eaves, nor should they be too LOW.
The way to check to see if gutters, downspouts, and landscaping are adequate, go outside in the next rainstorm. Watch the water on ALL roofs and in ALL gutters and down ALL spouts and on ALL landscaping. The water should be rapidly moved away from the home and NOT POOL anywhere where it can work its way into the crawlspace. When you get this rain, if it's gonna be a prolonged one, keep a loooong, watchful eye on the crawlspace, and see if you can tell where the water is coming in. This may help in diagnosing the problem too.
As far as a crawlspace getting wet in general, well, they can get wet as long as they drain quickly. If what you're stating in your post is that it's not normal for a crawl space to get 3" of water, and STAY with 3" of water for days, then you're right. THAT would not be normal. The water should drain out almost (and I say almost) as quickly as it takes to fill up. Problems arise when the water is allowed to pool in the crawl space for days on end. There is a specific way to size the space for air vents too. Ask your builder, and someone else who knows, what the proper sizing is. They should have vents! Perhaps someone else posting a follow-up can tell us.
I don't know what raking the visquine surface 'evenly' will do unless it's in the low spots only that you're seeing water pool. This measure may be OK but I'd feel more comfortable if you went through the 'tests' I mentioned earlier on about downspouts, gutters, and landscaping anyway. It may be crazy to put a sump pump in if raking the visquine and fixing the landscape (gutters and downspout possibly too) take care of the standing water. In short, if you get a LOT of water from a short, light rain, I'd suspect gutters and downspouts and landscaping. If you get a little water in a HEAVY downpour, this may be OK. You have 5 months to go on your warranty. Document everything and get something in writing from the builder as to what he's done to mitigate the problem. Definately take pictures when the space is dry (using a flash), and when it's full of water too (before-and-after). The builder is responsible for whatever the contract states. Read it again. The reason documentation and pictures are necessary is because when 12 months is up, if you continue to have a problem, you may need to prove that the crawlspace problem is an ONGOING one; not a new one! This philosophy of documentation and pictures goes for ANY problem you have while the house is still under warranty. Even if you have drywall nails popping. Take before-and-after pictures from all angles. If you only take them from one angle, you may not get a good 'view' of the problem. Trust me on this. The price of the film will justify any small or large claim you will possibly have after the 12 month warranty. And keep a house diary. It's a good thing to have even when you go to sell the home, and for court cases too!