Duplicate mails in Lion Mail - Where do they go?

I have three email accounts, 2 POP ones and my me.com address which of course is IMAP. I have the two POP accounts set to automatically forward all received mail to my me.com address, because it was an easy workaround in order to get them to appear on my iPhone & iPad. Needless to say this meant that on my Mac I would receive each mail twice (all three addresses flowed into a common inbox), but I felt it was worth the hassle and became totally comfortable with this in Snow Leopard. After the Lion upgrade, I switched to the classic view mode in the new mail as it's my comfort level, since I spend hours a day emailing, and now all the mails I get I only ever see one of them in my inbox. The thing is, I don't know where the other one is "going" and when I delete the one that's there I wonder where the other one is? Sometimes the one that shows up in the inbox is the one directly to my POP account, and sometimes it's the one forwarded to the IMAP one, and as yet I haven't been able to find a consistent reasoning behind which is which.
I'm sure this is some new helpful feature in Mail but I'll be damned if I can figure it out and I worry I may be missing something.
Another wrinkle that I can't find a fix for, and it's probably related, is that when I select a mail in the inbox list and then reply using apple-R (as I always would have) SOMETIMES it lets me, and sometimes it doesn't. By the same token the reply button in the toolbar is dimmed. This doesn't appear to be related to which address it was sent to (or forwarded to) and the only way I can reply is to open the message itself and then reply. More than anything this is driving me crazy because just a quick apple-R has been my method for replying for years now and it's yeah making me squirrely.
Please anyone any hints, or show me what obvious thing I am missing here?
thx

Maybe you should try de-activating the "Include related messages" preference in the "Viewing" section of Mail preferences?
Hope this helps

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