[GraemeJ]

That used to worry me a little as well - although the count is accurate, it is a little confusing visually (but nothing like as confusing as it was at initial release).  

I use the metronome as you do - to check that I'm counting in at the right tempo.  To overcome this minor visual problem, I simply changed the setting from "LED" to "Circle".  By doing this, you will lose the accent on the downbeat, but that's really not important.  In fact, I find it easier, since I can make any beat the first one.