I saw it mentioned, but wanted to give the thought a little more emphasis. When you let the SE-5 tranny downshift for you, for example, approaching a stoplight, you MUST completely let off the throttle! After finding myself stopped in 3rd or 4th gear a few times, and having to go through all sorts of contortions to get it to downshift, I finally trained myself that if I was going to come to a full stop, to take my hand off the throttle completely (this may not be comfortable for everyone, but it worked for me). Alternatively, you may want to consciously and physically return the throttle to the full off position. I have a tendency to let my hand roll to a comfortable position when letting off the throttle, but not necessarily all the way back to zero throttle. I don't know how many other people might be likely to do the same thing.
Whenever I'm actively moving around in traffic, or if I'm not sure if a full stop is upcoming, I always downshift manually. This advice is not for those times, only for when you are sure you are coming to a full stop, particularly, say, from highway speeds. The faster you are going (and the higher gear you are in) when the slowdown/stop is initiated, the more likely the machine to be confused if you continue to feed it even the tiniest bit of throttle.
Until I figured this out a couple months into my ownership, it was quite frustrating for me!