Same here, active customer service is pretty much unheard of, LOOKING for things to fix? Brilliant

You should definitely be above-board with Gamersgate, because they are remarkably above-board, conciliatory, and generous with their customers. I make liberal use of their support line with questions about their products (particularly concerning publisher DRM), and they've given me free stuff in the past as an apology for confusion or inconvenience. The staff there is eager to please, and I would feel bad ripping them off.

I would definitely report it. I almost guarantee you that you'll be rewarded in some way.

I have no experience with GamersGate whatsoever, but if they are really as nice to their customers as everyone here is saying, I say definitely report it. Excellent customer service should not go unrewarded. If we want excellent customer service (and we do), then we need to do whatever we can to promote that. Hopefully other companies will follow suit in time.

I agree with Navaho here...a company like Paradox deserves the honesty...D2D...that would be like getting undercharged at Wal Mart. I am pretty sure morality has no place within those walls.

Karma?

I might be thick but I don't get the situation. You mentioned you bought $40 of blue tokens... did you actually buy them and where are they now? Are you sure that those didn't go towards your order and the 44 cents weren't taken out of your account on top of those? Or did paying 44 cents get you those blue coins which you then paid for the game with?
Personally, I'd be honest and point out the mistake if there has been one. I'd do it in a way that leaves it up to them what they want to do, e.g. say they may want to check their shopping system as you were only charged 44 cents for Borderlands. Either way, I doubt if pre-orders are as binding as on the spot sales, so they may ask you for more money anyway, and you'd come off better if you voluntarily pointed out the mistake.

Honestly, in your situation I wouldn't feel bad at all about explaining your problem with the transaction fees as well. Be completely up front about everything. "Look, I was undercharged for the game and wanted to bring it to your attention...I am worried about being charged transaction fees a second time on my purchase when you change it, though."

This.
The way I understand it, the game was advertised as $40 but you were just charged too little. So they would be in the right anyway, and theoretically able to ask for the rest of the money later. Letting them know yourself beforehand might be the better choice anyway, considering what other people say of the company here.
I had a different situation once where I pre-ordered a $120 CD box for $10 because the store made a mistake setting the pre-order price. Thus, there was a binding contract between me and the store that they would sell it to me for $10, and they did. They noticed it and corrected the price a few days later but did not come back to me. I guess they could have claimed fallacy (is it called that in English?) and requested the contract to be revoked, but there were probably not enough pre-orders to make it worthwile. In general, the price you were shown while pre-ordering is what you agree to pay, so if it's just a billing mistake, better tell them.