Reinstall Nero and it should work properly again as long as your system is stable. When you reinstall Windows over the existing copy, you don't have the updates you once did, and more importantly for your programs, you don't have the registry entries that were created during the initial installation of the program. This can cause problems in some programs but may not have an adverse effect on others.
Once you do this, I would recommend backing up your data and scrapping the entire system and reinstalling Windows properly. It is also a good idea (especially with a HDD as large as the one you are using) to create two partitions. I generally use a 30-40GB partition as the C:\ drive for the OS and my main applications (Nero, Office, etc) and use the remaining space for the D:\ partition, where I install my games and store my important data. That way the next time Windows screws up (it will happen), I can simply reformat the C:\ drive and reinstall without losing my important data and saved games.