Transferring texture between Photoscan and Retopologised model.

This is the texture i get from the photoscan software.

This is how the texture looks when it is applied to the .dae model. Notice how in the darker painted part of the scan the geometry is very bumpy but in the light painted part it is much smoother, well, the part of the texture which i bake on the retop model which has the most problems (White squiggles) is the dark bumpy part (coincidence?).

When I bake the texture to the retopologised model I use blender render. The settings for the bake are “Bake Type” - Textures, “Selected to active” - On, Distance 0, Bias 0, Margin - 16 px, Split - Automatic

Its not the worst problem in the world because i should be able to take it into gimp and use a clone brush to fake it but i would prefer not to let me clumsy interpretation interfere.

Thanks for your help.

are you by chance trying to use the color image AS a bump map ?
that will NOT work .