(1) the important thing is that 3dClustSim ran and seemed OK
(2) you must be using an older version, since the output text format has changed somewhat, and more iterations are now the default
As far as the 'Bad fd number' error goes, it comes from the shell that is invoked to run the 3dttest++ -randomsign iterations. My guess is you are using Ubuntu, since that error message only seems to come from that type of system, and is due to the remarkable fact that they replaced the default bash shell with another shell that uses a different syntax.