The tonneau cover not gong up is a problem for a lot of us here. There are a few threads with the discussion of how to take care of it. Most of it has to do with the gas shocks and air temp(warmer is better, colder is worse).
The top alarm could be that the roof hasn't fully cycled up. Try running it down a little bit, and then all the way back up, holding the button until you here a bell sound, indicating the end of the roof cycle, and that it should be locked in place. If that doesn't do it it may take an adjustment of the roof stops on the up cycle side. L et the dealer do this to keep everything kosher with GM and let them (the manufacturer) see that there is a problem with yours.
Hope this helps.