OK, and this is the bug which I was previously experiencing sometimes and only now have nailed down. StartManager.pl can fail prematurely even though the master vm's config file is set right and the permissions are all 777. This is basically the same as one I mentioned over aim to Darien which looks like it might be specific to something in my setup. What I had mentioned was that if my master vm is registered in the console inventory then it crashes, so I was just removing the master before I started. But now I see that also it seems to crash early if a hash-named-clone is still registered from a previous run. Also, I will clarify that while the script seemingly crashes (that is, it drops me to a shell prompt after outputting the error), the script still appears to be running in the background as shown in the ps output below, and as seen by the fact that the clone that it was making when it crashed still seems to get all the way to booting up, it just never receives anything from the manager.
new-ghibli:~/HoneyClient-Manager-0.92 # perl bin/StartManager.pl www.cnn.com
Useless use of a variable in void context at /usr/lib/perl5/site_perl/5.8.8/i586-linux-thread-multi/IPTables/IPv4.pm line 5.
Starting new session...
VM Daemon Listening On: http://localhost:8089/HoneyClient/Manager/VM
Calling setMasterVM()...
Result: 1
Calling quickCloneVM()...
Result: /vm/edc639ee60d6255aa738d5ed2e/newwin.vmx
Calling isRegisteredVM()...
Calling isRegisteredVM()...
Use of uninitialized value in concatenation (.) or string at /usr/lib/perl5/site_perl/5.8.8/HoneyClient/Manager.pm line 478.
new-ghibli:~/HoneyClient-Manager-0.92 # ps aux | grep perl
root 12767 0.5 1.8 51520 38464 pts/2 S 21:20 0:01 perl bin/StartManager.pl www.cnn.com
new-ghibli:~/HoneyClient-Manager-0.92 # kill -9 12767
new-ghibli:~/HoneyClient-Manager-0.92 # kill -9 12767
bash: kill: (12767) - No such process
verbose output to follow