Yes, I very much anticipated these sorts of issues. We've introduced a whole slew of variables by relying on a third party product to work properly in a uniquely configured server environment.
Sorry you've sunken so much time into it. Two things I can say right now.
1) As seen in the bug reports thread, I am changing the exec() function to something more robust and compatible that may resolve the issue.
2) I'm also going to add a way to echo out the shell commands that are run, so you can go to your command line and try them yourself to see if it's just a bad command or if it's a good, working command that is being executed improperly, or not at all, by PHP.
I can tell you, though. I have it set up on two different servers for two different clients right now, and it's working awesome. Clients are nuts about it, too. If we can iron out these kinks, I really think we have a game-changer on our hands. :)