Here is a interesting problem, when looking at the pen even under bright light there are no white scratches, or spots, yet with a flash this is what a photo looks like......
Don't use a flash. The light is much too intense for macro photography, unless you have special units designed for that. Diffused, non-directional light is much better for photographing things like pens.
It sort of looks like the light may be reflecting off some underlying sandpaper marks in the wood.... easily overlooked in general difused light but seen in a more direct harsh light..... For what it is worth.....