I know what you mean sneaks, it's good for getting me started but tends to go off far too soon. I just ignore it, work through the break and then take a longer one after say two tomatoes (apart from anything I'm physically incapable of a five minute break, too short even to make tea!). Mainly I just like the encouragement of logging my progress so I can see that I'm getting somewhere.
I could do with that encouragement today, I'm so sleepy and the thesis just seems impenetrable.