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Windows allows you to globally configure the foreground and background colour for text in application windows, across all applications. Since PuTTY's own foreground and background colour are configurable anyway, it currently ignores this global configuration.
We should have a checkbox in the Colours panel which allows you to specify that PuTTY's foreground and background colours should follow the Windows default settings.
Update: Implemented on Windows (I've also taken the cursor colours from the system-wide config).
Audit trail for this wish.