Hi Andy,
Looking at what you had in 2012, I believe that everything worked properly during the migration to 2013.
In GlowPlug Washer 2012.ipt, your physical material was set to Default & you had applied a part level color override to make it look as you wanted by selecting "Copper (New/Polished)". This would be classed as an override in 2012, since the color of the Default material was changed.
When this is migrated to 2013, the physical material remains as Default, & the Appearance is set to "Copper - Polished", which is the best match to what it was previously. (This is the override mentioned below).
In your original 2013 version, you'd changed the physical material to be Copper & left the appearance as it was, (or perhaps with a few tweaks??). If you then remove the override, you return the appearance to that of the default for the Copper physical material.
All seems Ok so far (programmatically at least), & this explains why you can get these 2 parts to look the same by removing the overrides - they both go back to being Copper.
So if you want to preserve your "tweaked" copper appearance, you have 2 choices:
1. From the Appearance Broswer, Rt click on the "Copper - Polished" appearance & use Add To & write it back to the Inventor Material Library, essentially updating the master appearance.
2. Create a custom appearance library & then use Add To & copy it there instead - might be worth giving it a different name so that you know it's your modified version.
Note that if you decide to create your own custom appearance/material library you should edit your project file, to include it & make it active. Note that you can have a single custom library that contains both physical materials as well as appearances, or keep them separaate if you prefer.
I hope this is clear, (as mud ?); it's reasonably well documented in the wiki help, but this probably shows that we need to provide some better info there too.
Thanks,
Chris

Chris Mitchell
PDMS Customer Engagment Team
Autodesk, Inc.