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Staining after toneing

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Apparently, when I put the paper in, it occasionally scrapes the bottom, the brown stuff at bottom of the tray transfers, and become more visible once paper is dry.

Could that be your problem??

Such effects that might be barely visible on a straight print can have dramatic effects when toning is done. I experienced this during a Tim Rudman toning course, where the texture on the vertical sides of my well-cleaned Nova processor became visible on prints only after toning.

In this case, careful and regular agitation solved the problem.
 

Add bad paper to that. There was a batch of Forte PW14 which was known for a simlar but uniform stain from contamination with metalic silver in the emulsion.