OK, here's another weird intonation issue I'm having. Let's say I have tuned up and I'm able to play a high Bb concert pitch (Bb4) in tune. When I play an A natural (2nd valve) it's horribly out of tune according to my tuner app on my iphone. When I say "horribly" I mean almost a quarter step flat! Ab (1st valve) is also flat, but not quite a bad as A natural. And I can't lip those notes into tune no matter how hard I try.
The thing is, 2nd valve and 1st valve notes are fine in other registers.
Can anyone offer some insight as to what is going wrong?