If I "hear" the noise, I switch gears. But that never happens in the situation I described (middle ring, lowest cog). It does happen once in awhile when I need to actually switch to the big ring. Mostly, I think once you known the "feel" of your gears, you learn which ones you should be using.
I had a lot of problems with the Ultegra on my Trek 5200. In fact, I could not get the front into the big ring hardly ever, until finally, my DH put Dura Ace on there. I am not sure why this was happening, but it did cause a lot of dropped chains. I am very good at getting it back on, without getting off the bike and stopping because of this!