Have you asked them to tune so quietly that they can hear the person next to them? Seems obvious but isn't it true that a lot of amateur groups tune waaay too loudly? Edit: one comment is that we find that sections don't like to be "shown up" by other sections. So get them to play a passage together while everyone else listens; if their intonation is poor, everyone will know and you can bet they'll try harder. Then just start building, section by section. If you can play back a recording of them, they'll be able to hear the problem areas (not having to concentrate on playing at that moment) and will have a better idea of where "issues" are coming from. Things tend to go past pretty fast in concert or rehearsal and don't get noticed as much as when you concentrate on listening to a playback.