When making biodiesel from different oils from different restaurants the colour of the resulting fuel is either dark or light in colour. I assume this would be the result of the different foods cooked in the oil, and/or the amount the oil has been heated and cooled.
When left for awhile in a container this "colouring" seems separate. When left in an open jar it fades. When in your fuel tank there seems to be a film around the top.

Can this be eliminated by using a neutralising additive?

In my experience, bio made from saturated fats is lighter in colour than when made from something like cottonseed oil. It's nothing to do with impurities - just the natural colour. Don''t quite understand the rest of your post.

Bio made from new oil is a lot lighter than used oil.

Also the colour of the oil had a bearing on the colour of the finished product.

I don't think the varying colour is anything to be concerned about.

I've never really had a look inside my fuel tank to see what's in there.

The used veg oil from Thai restaurants is quite dark in colour. Probably from the colour of the spices they use in the cooking. Even after several months of settling the colour remains. I imagine it would remain even if the oil was reacted to make bio. I filter to 5 micron and then leave the filtered oil in plastic containers for months again and although the dark colour remains I do get a fine powder? settling in the bottom of the containers. seems to be less than 1 micron so I am assuming it is not harmful but who knows? I wonder if powder washing would remove the spices (if that's what it is) and lighten the colour.

Interesting - I make biodiesel using waste canola oil from a Thai restaurant and it is also very dark in colour (and smells like spicy peanuts). Like you, I let it settle then filter (jeans leg filter), let it settle some more, pour off oil for transesterification slowly, leaving a very fine sediment behind. After processing the biodiesel product is still rather dark, but I filter to 1 micron, it passes the tests and I assume it is OK. Hasn't caused a problem yet (1996 Holden Astra X17DTL).

I haven't tried powder washing but have some Purolite that I was going to try (but that is more for removing any traces of soap, lye, methanol or water). Also considered activated carbon as I have used it in the past for decolorizing organic solutions. Maybe it would decolorize biodiesel?