Is it obligatory to give charity amounting to the value of a genuine Windows program, or the amount paid to the shop after realizing it was loaded with a "crack"? And is it obligatory to give charity for every time the program was loaded, given that there isn't enough money available?

If you were unaware that the software you used was pirated, there is no sin upon you. The sin falls upon the one who downloaded it without informing you. You must stop using it in the future to cease engaging in the unlawful. Some scholars permit the use of pirated software for personal benefit when needed, not for earning money.