Is this Arduino MEGA 2560 R3 a counterfeit?

What you can do...

http://arduino.cc/en/Main/ContactUs
Search for "Trademark Violations". It's close to the bottom.

If you believe the "Made in Italy" board was not actually made in Italy (e.g. shipped from Szechuan) you could try reporting it to the Federal Government. I believe this is the right form...
https://apps.cbp.gov/eallegations/

Stop doing business with Amazon (obviously ;))