Thanks.
I know this graphical patch that you mentioned. It fixes the "unclickable object problem" for ATI cards and able to increase the resolution for more than 1024*768. But unfortunately this patch isn't solving the Direct3d problem in new Nvidia cards and the new resolutions are only available if you are using this Direct3d mode. So, if you are still experiencing problem in Direct3d after appling the graphical patch (which is the case for me), I'm afraid you are stuck with 640*480 and software mode.
My hope is that if we can communicate with this person who made this graphic patch, maybe he will be able to solve this problem with new Nvidia cards.