The painting list for U-boats in Anstriche und Tarnanstriche der deustschen Kriegsmarine (Painting and Camouflage of the German Navy) states that the wooden deck was treated with a wood preservative (Teerfirnis Tf 99). This made the deck start out as black in colour. As it was exposed to the elements, the deck would quickly become bleached by saltwater and the sun. This would give the deck a muddy grey colour with a brown tinge. The more the deck was subjected to weathering, the lighter and browner it would become. Areas that were walked upon would have become more worn, and thus browner. In addition, a wet deck would look darker than a dry one. Also, small patches of white (caused by bleaching) may have appeared on very weathered parts of the deck. Lastly, there may have have been small patches of green slime.
Rainer Burns has done quite a bit of research on the wooden deck colours. I think it was him who said that teak was too expensive to be used on U-boats, so cheap local wood was used instead. That would explain why the decks didn't look like weathered teak.

Regards,

Dougie