I just received a Total Remote today, and I've discovered the same thing Mike is seeing, with a twist! I have 3 SA 3100 boxes here, and 1 2200. Using one of the included profiles, I can control 1 of the 3100 boxes. The same profile does nothing on the other 3100s or the 2200.

So, I think the problem lies with the boxes, and not Total Remote. Weird stuff.