To reproduce, create a .cpp file with the following two lines:

aaa = 1; // xxx
b = 2; // yyy

select everything and 'M-x align'. Result here:

aaa = 1;                        // x
b   = 2;                        // yyy

The first comment is half-eaten.

Version: GNU Emacs 24.3.50.1 (x86_64-unknown-linux-gnu, GTK+ Version 3.8.6)
of 2013-12-17 on gonzo.localdomain

Paul