There is a thread on the eclipse plugin
http://arduino.cc/forum/index.php/topic,79595.0.html
I noticed this today as well. The reason is that what you see is in Juno while the other is in Indigo.
The bad news is : In Juno you can not set this option anymore
The good news is that after a compile and a rebuild of the indexer Juno sees the Serial.
Best regards
Jantje