Server Mail will not delete - tx.rr and Network solutions

I have an iphone 4s.  My first iphone.  I have two email accounts set up.  Both of them are setup to delete from server when delete from inbox.
They are not working.
I have called apple and the pop 3 providers and neither can help.
I have tx.rr.com - road runner and Network Solutions (company I have a domain name with).
BOTH of these have worked corectly with my last two phones, Blackberry and Samsung Epic.  But neither are working with the iphone.
Is anyone else having this issue or suggestions on what to try.
Of course I want to get apple and road runner on the same call so I don't keep getting sent back an forth to each one.
I REALLY want to be able to delete from the phone as I get so many emails due to my personal business...I want to be able to delete all day long and not have to go home and read/delete again.

Yes, it was definitely within Cyrus. The Apple interfaces are pretty and all but they didn't even get close to helping me solve this easily.
Essentially, what I did was download all the emails from the server (to make sure I didn't miss anything), rename my email folder to something different to preserve the emails in case I really did miss something, then do a recover on the mailbox.
Being a UNIX-head, here's what I did on the server:
cd /var/spool/imap/user
mv scott scott.dead
sudo /usr/bin/cyrus/bin/reconstruct -r user/scott
Sudo, of course, prompted me for the superuser password but everything was fixed right away after that. It is recommended to shut down the mail service from inside the Server Admin program first.

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