No issues in particular with the early cars, some Cooper S do suffer from a cold start clatter noise but its not confined to early models.
Yep, the R56 started production in September 2006, its the 2007 model year.
FYI Most of the early UK dealer demo cars were laser blue with white details. I'd wonder if it was a dealer demo car or a press car. If so you can pretty much gurantee it wasn't run in as per the manual!