I've noticed that one of my own workflows stopped working after the current update, then I've created a new workflow and experienced the same behaviour.
It seems to me that "Terminal Command" is broken. Even the most simple "ls" command freezes Alfred for about 10 sec then returns without any warning/error (just as if everything went fine).
I've even tried debugging, but it only says that a command was executed (no warnings or anything)
Alfred 2.2 (243)
OS X 10.9.3 (latest beta)