I suppose it could be an issue of someone turing eevrything ON with the remote and then using a different remote to turn off. That would leave the Harmony confused.
You need to hide the other remotes so family members will not use them in place of the harmony. My dad had the same problem, swore that the harmony was a piece of crap. Then figured out that my mom was using the original dish remote sometimes and screwed things up. Once we got my mom to use the Harmony instead everything worked perfectly. The harmony remote only remembers the last state(on or off) that IT left the equipment in.