Thank you Filip, I also exchanged a few emails with Vlk in regards to this issue and I can add that when the SMS commands are visible the problem is not caused by using GoSMS, (as I use Handcent) Commands are not sent via internet SMS portal, (I have tried commands from 2 different phones) and Anti-Theft is activated (I would assume because I receive the returns from the commands. ie "2222 locate" returns a map link)
I've used the paid version of Theft-aware since June of last year without a problem and just switched to Avast! a few days ago and now all the commands are visible. I'd hate to lose my phone and tip someone off with a "2222 Locate" command. I can't seem to figure out what's going on and I feel a bit vulnerable now about misplacing my phone when I go out. At least I can remote wipe, but ideally I'd like to be able to track it down (which I did last December when I left my phone in a cab)
I really believe in this app and I know it works!