I have trialled a Garmin 12 against a KLN900 and got the same, even at speeds around 400kts groundspeed.
Was your handheld one of the old 8 channel ones perchance? That might have made a difference - it might have had to use satellites lower to the horizon as they are the only ones they could see. Lower to the horizon means more error.
Mind you 16% sounds a lot!
CS