Version:           4.2.00 (using KDE 4.2.0)
OS:                Linux
Installed from:    Unspecified Linux

This behavior occurs on an archlinux system running KDE 4.2.

System Settings prompts for apply/discard when it should be unnecessary.  For example, if you open System Settings > Appearance > Icons and select another theme, then the one you were originally using, it will still prompt you to save/discard/cancel.  This happens with every setting for which I do the same general procedure: select a different option, then go back to the old one.  It even happens if you open up the font config, select 'choose' to change the font, and then confirm the exact same font you had before (merely hit 'ok').

Proposed solution: system settings 'remembers' what the original settings were when the kcm module was loaded and only prompts if the settings are different when exiting the module.