lion recovery startup

once in a while when i start-up my macpro, osx lion, it will open with the scree that says i need to use lion recovery / time machine and two other apps, like theres something that happened on shut down. i hold the power button down on the tower for 15 seconds or so then wait 10 seconds and start it back up, everything is fine then. cant think what would cause this to happen. its like something as happened to my hard drive. kinda of scary for it to do this. now im not computer smart so what i did was to clone my first hard drive to my second hard drive. i figured if one is corrupted then i could start up from the second. then erase the first and copy from the second back to the first. i know most people use a external hard drive for backup but no money for that now. any thing wrong, im sure there is, in doing it the way im doing it ?