I'm still unsure as to what caused this in the first place; you'll notice that the "welded appearance" bolt has a Material of Steel, Mild & an Appearance of Default. The proper looking bolt has a Material of Steel, Mild and an Appearance of Steel.
If you view the assembly using the Realistic view mode instead of just shaded then it will appear correct. I suspect this will be the case for your other parts too.
Do you recall if when you first opened the data, whether you had configured a custom appearance library or if you were just using the as shipped versions ?
Chris Mitchell Inventor Quality Assurance Team Autodesk, Inc.