I see the same relationship in data between my wired bike computer and Cyclemeter. Usually the data from Cyclemeter are a little more liberal, i.e. smaller ride time, larger distance, larger average speed. I record both sets of data in my log, but I have chosen to use the data from the bike computer "for record" because it's a little more conservative. Also, Cyclemeter, on rare occasions, has a brain fart. With that in mind, I consider the bike computer to be a little more reliable and use it for my "official" records.

Chose one or the other, don't sweat the diff, and enjoy the miles.