2003 has 10 colors and 2007 has 12.
If you’ve converting a file from 2003 to 2007, 2007 adds two new color “locations”, but re-positions the 10 colors from 2003 somewhat randomly to the new 12 location scheme in 2007. That means the next time you need a new shape, getting the correct color becomes unpredictable.
Naturally, you can re-organize the colors, but in a large company, people share things without thinking of version issues and the issue may not be noticed until a top exec is nearly ready to go on stage and asks for a change in his presentation. The designer being asked may not be aware of the color shift and it could be an embarrassment for everyone involved.
More on this is coming. We suspect it could be a bug, but we’re checking into it.