What kind of extruder are you using. The bushings on the old Mk II tended to generate a really fine black iron grit some of which got into the extruder barrel with the filament. That could darken plastic. If you are using one of the old threaded bolt or rod filament pump designs take the extruder apart and see if you have a lot of black iron dust inside. If you do, that may be what is causing the grief.
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Hell, there are no rules here - we're trying to accomplish something.
Opportunity is missed by most people because it is dressed in overalls and looks like work.
Thomas A. Edison