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