I doubt that anyone understands it, to tell you the truth. I'd estimate that 99.99 percent of all my email support tickets and calls relate to iThings. I think the last non-iThing mail ticket I got was about two or three years ago -- and I'm not even kidding.
All of my servers support BlackBerry FastMail, so setting that up is a no-brainer. Email address and password, and the device auto-configures. Android requires a bit more work, but ultimately works. Same for Outlook, T-Bird, etc. But iThings are hit and miss. Even if the user does everything exactly right, it's a crap shoot whether the mail will work.
Another annoying thing that I have to believe is caused by unannounced updates is that some days, I'll get a bazillion mail complaint tickets from iThing users, all on the same day. Previously-working mail will simply stop working, for no apparent reason, and with no fix other than deleting and re-creating the account on the device using the exact same credentials and settings. I have no idea why this happens, but I have to suspect silent updates. I can't think of any other reason.
The mail, in fact, is the main reason why an iPhone will not be my first choice when John Chen finally drives the last nail into BlackBerry's coffin. I like Apple's emphasis on privacy, and I can tolerate the rest of the OS, but the mail is absolutely ghastly -- and for me, mail is the most important feature on a phone other than voice.
I don't know the specific reasons for your problem. I have to believe that it has something to do with the way the iThing's IMAP implementation handles trash because my users have the same problem. There doesn't seem to be any way to completely delete the real crap that they want really gone. I happily bulk-delete it for them server-side when they ask because it hogs storage space on my servers.
Other than using POP3 (which takes some doing on an iThing and has plenty of its own drawbacks), the only thing I can recommend is logging into your mail provider's webmail gateway and seeing if they have a way to remove the offending messages. I'm sure there must be some other way to really, truly delete an email using an iThing, but I haven't found it yet.
Rich