Question mark flashes briefly, apple icon, computer starts?

After replacing the hard drive my computer works good however when i turn it on a question mark in a briefcase appears briefly then the apple icon appears then it all goes normally, I would like to know why this happens, my understanding is that the question mark means that their is a problem i just don't know what it is or where to look for it?. Also I had to replace my old battery (as it wasn't charging) and now if I leave the charger unplugged, the computer shuts of after awhile and when i power it back on it starts of where it was at as if its asleep but i actually have to turn it back on, I don't know if this has anything to do with it each other or if it is 2 seperate problems..?