Check your Photoworks Options.
Make sure the "Overwrite Solidworks properties" box is un-checked in the Systems Options menu.
Per the Help file:
Overwrite SolidWorks properties - Select this option to overwrite the material properties of the SolidWorks model with the properties of the PhotoWorks material. When this option is cleared, the SolidWorks material properties are unaffected by the PhotoWorks materials.
For example, if you select the check box and select a Green Metallic Paint material, your model turns green.