I feel that something could have gone amiss the way you had installed Windows7 first with a non-genuine copy and then with a genuine copy.
To confirm that there is indeed a problem, I would suggest
1. Disconnect your optical drive from the system - both the power cable and data cable.
2. Do a clean install with the genuine copy of Windows 7 from a USB pendrive. ( Do not activate at this point. You have 30 days to do it.) And do not forget to back up any data that you may not want to lose.
3. After install and you are sure that Windows is booting up without any problems, connect your optical drive and then start your PC. Check whether Windows recognises it and report whether you still have the problem.
In short, you will be starting off with a pristine Windows7 installation, without the optical drive and connect the optical drive afterwards.