Im using IDE 1.0.1, yes Ive seen the reference, its not a big deal really, as I just add an extra read to deal with nl char.
But, I do like to understand why things don`t work as expected.
In the serial monitor you type 12 and press the enter key or press send.
This means there are three chars in the buffer waiting to be read, ascii 1, 2, and the new line char, the code reads the first two chars, leaving the nl char in the buffer, so I would assume that Serial.flush would have cleared the buffer of the nl char, but it does`nt.