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If Windows 95 is installed over an older version of Windows, it scans SYSTEM.INI, WIN.INI, CONTROL.INI (used by Control Panel), PROGRAM.INI (used by Program Manager) and WINFILE.INI (used by File Manager), and incorporates much of the information it finds into the new Registry file. But these .INI files don't disappear. They still exist for compatibility with Windows 3.x applications.
Every time Windows 95 loads, it checks these .INI files, looking for new information stored during the installation of older applications. Windows also monitors changes made to the .INI files while it is running. When new information that belongs in the Registry is detected, it "sweeps" the .INI file entries into the Registry. Some are left behind for compatibility with older programs, but many are removed from the .INI file when Windows has finished its sweep.
So if certain .INI file entries keep disappearing, or if Registry entries you've just deleted have mysteriously reappeared, you're probably not seeing things. It might just be that busybody Windows at work.
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