Before you initialize or reformat, take the time to search for an extension or software conflict. Reinstall the system software. Simply boot with the installer CD and run the installer. If the problem occurs only when you try to launch or run specific applications, check the publisher's web site to see whether there is a later version available. If all else fails, then consider initializing or reformatting.
Initialization writes a new, blank directory.
It knows nothing. But initialization does not erase your data. It is quite possible to recover most or all the data from a disk that has a corrupt directory, or a disk that has been accidentally reinitialized, by using one of the disk repair utilities mentioned above. Reformatting erases all data. It wipes the disk clean.