I have run into a similar problem over the years beginning with VW 8. It has usually been caused by the corruption of individual classes. You might find that one, two or three classes contain the objects that are behaving this way. Those classes have default pen colors, fills, etc. The corruption induces the application of those attributes (pen colors, fills, etc) to all of the class contents. Try deleting one of the corrupted classes - while being sure to assign the contents to another class. You can then create a new class with the same name and re-assign the objects to that class. Its worth a try. Good luck.
20" iMac Core Duo
VW 12.5