I wanted to make everyone aware that due to the new way of working with materials and appearances/colors in 2013, extreme caution has to be observed when migrating custom Content libraries that contain custom materials.
The order in which you do things is of utmost importance. The proper migration order is:
1. Migrate your custom material style into a 2013 material library first
2. Make sure that the proper material library is active in your project file
3. Update the content center library
I'll give a more detailed example of each of these steps.
Assume that I have a Content Center family defined in a desktop content file Mylibrary.idcl that uses a material called "Glowing red uranium".
Why uranium? I like to live dangerously J

Fig 1: Custom Content family with Custom material
I'll describe two possible scenarios.
Scenario 1: the custom material is defined as part of your Materials.xml and Colors.xml file in 2012 and you want to migrate the custom material into the existing InventorMaterialLibrary.adsklib library.
Scenario 2: the custom material is exported in 2012 as an individual style file called glowingred uranium.styxml and you want to migrate this style to a brand new 2013 Material library.
Step 1. Migrate the custom material style to 2013
This can be done quite easily by using the Migrate Inventor Styles option at the bottom of the Material editor window.
The only downside is that you will need to start a new Inventor part or assembly file to gain access to the Material and Style editor.
Scenario 1:
Start a new part and start the Material editor
Start the Migrate Inventor Styles command

Fig 2: Location of the Migrate Inventor Styles command
Select as origin location the folder where your Materials.xml and Colors.xml file sit.
Select as destination location the folder of the InventorMaterialLibrary.adsklib , which is by default in C:\Users\Public\Documents\Autodesk\Inventor 2013\Design Data\Materials.

Fig 3: Migrating material style to existing 2013 material library
Close and reopen your Material editor and you should now see the custom material show up in the list

Fig 4: Custom material correctly migrated
Scenario 2: if you have an individual file glowingred uranium.styxml that you want to migrate to a new library.
First create a new material library and call it Mylibrary.

Go to the Style editor and Import the style

Fig 5: Import button allowing more granular style migration
If you open the Material editor, you will see that the imported material is showing up in the top portion of the dialog, indicating that the material is cached as a local style in the active document.

Fig 6: Locally cached material style
This means that our custom material is not in the library yet. To get it in the library, you would have to explicitly tell Inventor to add it to our library with the "Add to" context command.

Fig 7: Adding a custom material to a new library
This brings us to step two which involves some work in the active project file.
Step 2. Make sure that material library is active in your project file
Close all documents and open the project editor
For Scenario 1: make sure the Inventor Material Library is the active library
For Scenario 2: add the Mymaterials.adsklib file and make it the active material library (in bold)

Fig 8: Verifying in the project editor that the custom library is active
Step 3. Update the content center library
Keep your project file open and add the custom content center library (mylibrary.idcl) by clicking on the lower right icon in the editor.
The library will be flagged as being out-of-date by showing a yellow exclamation mark.

Fig 9: Warning sign that My Library is out of date
Hit the update button at the lower right of this dialog and you are set.
To fully test that your content center library works correctly, start a new assembly and place a part from the "My Library" library or you could also check the material in the content center editor of course.
Hopefully above procedure will spare you some headaches.
The bottom line is:
Please make sure that your custom materials are migrated correctly BEFORE hitting that update button in step 3.
Migrating the custom material to 2013 after the content center library has been updated to 2013, does not work unfortunately.
Thanks
Bob