Synchronizing iPhone and Mail.app inboxes
I don't think it's an iPhone configuration problem.

Maybe a Mail.app problem, it seems it's no syncing back the changes correctly. Except I don't think there's a preference to change that.

It's most likely a server configuration problem.
To be sure, we'll need more information about your mail servers. Do you have access to the configuration? What is maquib.com? From the look of it, it looks like your personal server (with a project to make a Mac OS Tiger app!)



Can you try to download Sparrow? (there's a free version)
Add your account on it and see if the problem is still there. That way we'll know if the problem is on the server or on the software side.