Email disappearing from iPad when I download in iMac

My wife is having the problem that looks like the ISP's (GCI.net) email server is deleting email from my iPad.
With her iMac off, when she is traveling, she can download and read email on her iPad. All the email stays there, unless she intentionally deletes something.
BUT, when she get home from a trip and goes to check email using Apple's Mail on her iMac, which is set to "Remove from server ...," she can WATCH as the email disappears from her iPad -- I have watched this. This has been very frustrating, as I have tried everything I can think of to no avail. My old PowerMac and my older iPod Touch has no problem with GCI email. I have gobs of savedemail on the iPod with the same Mail settings on the PowerMac (I do plan to upgrade to an Intel Mac, this fall, btw).
Searching the web and here inthe Apple forums, I have so far not found anyone with this situation. It acts like the email content on the iPad is only what is on the GCI.net servers. When my iMac removes those, they disappear from the iPad. But, I seen no settings on the iMac or iPad that will fix this. I have tried everything I can think of.
Her Gmail account works fine on her iPad.
The iMac is set up with POP account. (As is my PMG5). The iPad was forced to set up a POP account (as a possible solution) for GCI email because the default IMAP is where we first discovered the issue of the server appearing to delete email from the iPad.
Thanks in advance for your help.

Some of the older 30-pin-to-USB cables have catches on the iPad end. The connector block on them extends further from the iPad than the ones without the catch; they are almost square. You have to squeeze the sides of the connector to disengage the catches.
I'm not sure what being in iTunes has to do with it, though.

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