Many banks and card companies will place a hold on your account for the amount of a purchase, even if it is not immediately charged. This hold will typically be released in 24-48 hours. That is most likely what you're seeing.

It is still misleading, though.

It has nothing to do with us, however.  There is no money changing hands.

My understanding is the process goes something like:

1. You tell Stardock you want to pre-order the game so you give them your credit card number.
2. Stardock goes to your bank and says, "Do they have $40 in their account?"
3. The bank looks at your account, sees that you have $40 in there, and then tells Stardock, "Yes."
4. At this point the bank makes an assumption that in response to their "Yes" Stardock is going to follow-up with a, "Please charge them $40.", because from their perspective why else would you ask if the person had $40?
5. Stardock, however, doesn't tell the bank to charge you $40, instead it places the game on hold for you and then when it is released they will charge you $40.

Stardock is doing things correctly by first checking if you have the money before charging you, otherwise you could end up with an overdraft fee if they just charged you without checking first.  Your bank is the one that is setting aside the money, even though no charge is being made.  In most cases though, what the bank is doing is also good practice, because by setting aside that $40 (when someone checks to see if it's available) you don't accidentally get hit with an overdraft by purchasing two things at the same time.

In a perfect world, there would be a way for companies like Stardock to check for money but don't put a hold on that money.  That way Stardock could ask the bank, "Tell me if they have $40, but don't put a hold on that money right now.".  Then the bank would know that a $40 charge will not be immediately following the balance check.

Or I could be totally wrong about how the whole thing works.

Read: http://en.wikipedia.org/wiki/Authorization_hold

This is probably what happened. The Stardock servers put an authorzation hold to validate that the credit card is legitimate. Same thing happens when you use your card anywhere else. The merchant puts an authorization hold on your card until they settle the charges with the credit card company. If no charge comes through the hold will typically fall off your card in the next 5 days.

The only charges that I have seen be completely different is buying gas or eating at a resturaunt. If you swipe your card at a gas pump your card will have an authorization hold made for $1 just to make sure the card is legit. Later, you will be charged for the actual amount of gas pumped. Resturaunts will typically place a hold on your card for the total plus 15% gratuity. Again, your card will later be charged the amount you authorized.

Probably easier to bring your friend to your computer.

i really REALLY wish online retailers would RELEASE the auth on a card after doing it. this isnt a stardock problem, it happens across the board, and theres really no excuse for it. pretty much all the online CC processors ive worked with support auth reversals...