Disappearing GMail messages with Apple Mail for iPad

I'm using Mail for iPad to access my GMail account. When I organize messages into different folders using Mail, I often find that some of those messages simply disappear, unless I search for them. This happens regardless of when they were sent (they're not older messages cached on the server).
As an example, a message I received Sunday was placed in a folder. When scrolling back through that folder, the message does *not* appear anywhere, not between the Monday and Saturday messages. However, if I search for that sender, the message *does* appear and says it was received on Sunday, as it was.
I wish I understood why this is happening, as it doesn't seem to make much sense. Thanks for any help!

I have each device to leave message on the server.  We have it set up this way so that my wife and I can see all the mail that comes into our own devices.  Then we can delete off each device as desired.  I go in to the server once a month and delete old mail.
So to recap:  My wife's macpro uses apple mail.  it retrieves the mail from the server; but leaves it on the server.  However, though the email is still on the server, the other devices cannot retrieve the email.  it is like the email is old email that your device has already uploaded; but it hasn't uploaded to the other devices because my wife's mac opens the inbox on server first.
I know that this sounds confusing.  it did not always work this way.  for a long time any of our devices could open the inbox on the server, retrieve the messages and leave the email on the server inbox for the other devices.  this issue is new.

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