go into settings and about 1/2 way down or so you will see a section titled "Store" go in there and make sure the "Apple ID" you have matches the ID you used to purchase the app's.
you can use whatever other ID elsewhere just that one needs to stay the same or you will be charged again.
yeah the new dock connector is no surprise. Its been talked about for some time now but im sure apple will make a 30 pin conversion adapter. If apple doesn't make one theres plenty of 3rd party manufacturers will have one.