I've noticed that with our whistle player too. Bottom D is in tune with my open D, but the higher up the scale you go the farther out of tune it is. Think it means the holes weren't drilled accurately.
And it's only really noticable when we do a duet with him leading, so we don't use the cheapo's for that anymore. He has this really neat 3 pc. brass whistle that we use for duets.