Unusual problem, my mail in inbox dissapears!

Hi,
Just got an new Mac Mini. Imported everything automatically from my old G4 onto it. But....
My Mail Inbox is acting strange. ALL THE OTHE MAILBOXES ARE FINE, but the inbox shows I only have 91 messages when I used to have around 1000!!
On top of this, a random selction of messages in (and only in) the inbox don't display and instead show in italics something along the lines of "message cannot be displayed as it cannot be downloaded until account is taken online" or something along those lines.
The thing is, the account IS online and is working fine in all other aspecs. It is a POP3 account.
I have tried re-importing manually. No luck.
ANY IDEAS ANYONE? I NEED MY MAIL BACK!!!!
Thanks

Hi RedHavoc.
Not sure what makes you think this is an unusual problem. Actually, it's quite common. The conversion from Mail 1.x to Mail 2.x is broken. Take a look at the following thread to better understand the problem:
Help! "You need to take this account online in order to download it."
In particular, you may want to take a look at the following article (also referenced in that thread) to learn what you might have done before upgrading to minimize the risk of this happening, and what you may do after fixing the problem to avoid similar issues from happening in the future. DON'T do now what the article suggests, though, as that would make things worse in the current situation:
Overstuffed mailbox is unexpectedly empty
More specifically, if this is a POP account, the following procedure should allow you to fix the Inbox problems:
1. Quit Mail.
2. Make a backup copy of the ~/Library/Mail folder, just in case something goes wrong while trying to fix the problem. You can do this in the Finder by dragging the folder to the Desktop while holding the Option (Alt) key down, for example. This is where all your mail is stored.
3. Create a new folder on the Desktop and name it however you wish (e.g. Inbox Old). It doesn't need to have an .mbox extension.
4. In the Finder, go to ~/Library/Mail/POP-username@mailserver/INBOX.mbox/.
5. Move the files mbox and Incoming_Mail out of INBOX.mbox, into the Inbox Old folder just created on the Desktop. These files contain all the messages that were in the mailbox before the upgrade to Tiger, and maybe even some messages that had been deleted. mbox is the most important. Incoming_Mail may or may not be present.
6. Move any strangely-named Messages-XXXXXX folder to the Desktop (not into the Inbox Old folder). These folders are to be deleted after fixing the problem. They are temporary folders created during an import or an indexing process, and Mail should have deleted them when done. Their presence is a clear indication that something didn't work as expected. If you've been using Mail after the conversion and have already tried to fix the problem by rebuilding the mailbox or something like that, they might contain messages that are neither in Messages proper nor in the mbox file, so keep them around until the problem is fixed.
7. Move everything else within INBOX.mbox, except the Messages folder, to the Trash.
The result of the above should be that INBOX.mbox contains the proper Messages folder only, and the Inbox Old folder on the Desktop contains the mbox and Incoming_Mail (if it exists) files only. Now, proceed as follows:
8. Open Mail.
9. The account's Inbox should properly display in Mail as many messages as *.emlx files are in ~/Library/Mail/POP-username@mailserver/INBOX.mbox/Messages/. If that's not the case, select the mailbox in Mail and do Mailbox > Rebuild.
10. In Mail, do File > Import Mailboxes, choose Other as the data format, and follow the instructions to import the Inbox Old folder that's on the Desktop. Do with the imported mail whatever you wish. You may move to the account's Inbox the messages that Mail failed to convert properly, and delete those that did get through and, hence, are duplicates now.
The following collection of AppleScripts has a Remove Duplicates script that can be useful for removing duplicate messages:
http://homepage.mac.com/aamann/Mail_Scripts.html
If all is well and you're not missing anything, the files on the Desktop can be deleted, although you may want to keep them for a while, just in case.
Ask for any clarifications or if you need further assistance.
Note: For those not familiarized with the ~/ notation, it refers to the user's home folder, i.e. ~/Library is the Library folder within the user's home folder.

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    First off, IF you're using OS X 10.8.2 (Mtn. Lion) and Mail (6.2), the com.apple.mail.plist is NOT in the "usual" expected location.  Thanks poster Thomas A Reed, the com.apple.mail.plist can be found here:
    ~/Library/Containers/com.apple.mail/Data/Library/Preferences
    This was a BIG help.  But in my situation, the com.apple.mail.plist file was not there.  Instead, I found "com.apple.mail.lockedfile".  But even after I deleted it, Mail still wasn't working currently.
    So, I decided to go back in time.  Thankfully, Time Machine does come handy at times.  I was able to get the com.apple.mail.plist file in Time Machine from a date prior to the problem.  But even this "new" plist file didn't help.
    So, be it "voodoo magic" or just that God was on my side, I tried a couple of other things...
    First, I took the mailbox offline (Mail's Mailbox menu > Take All Accounts Offline).  As I even tried taking things offline, but going back online didn't initially help.  But I took it offline again.
    I then tried going back to into the Account preferences (Mail menu > Preferences > Accounts > Account Information) and changed Alias to icloud.com, instead of mac.com or me.com, and typed in the correct password.  I made sure that the Outgoing Mail Server (SMTP) was "smtp.mail.me.com".  I went into Advanced and typed "imap.mail.me.com", made sure that Port was "993", checked Use SSL, and Authentication to Password.
    I click to to another of Mail's preferences to bring up the Save dialog.  And when I clicked Save, it did not click.  It saved for the first time.  No error message at all.  A positive sign!
    So, I then when to Mail's Window menu and selected Activity and when I selected to Take All Accounts Online, I could see that everything was working!  Yeah! Mail was now working as expected.  It was an awesome sight!
    Now, please remember that these are my observations.  May this be a hopeful guide to your situation.  I cannot swear that this is THE solution, but something worked for me.  Like I said, maybe God was smiling on me as the problem with Mail was on my wife's MacBook Air.  So, Mail is now working, I'm happy and ultimately, my wife will be happy now that she can use her Mac like she expects it to work... 

    I have completley reinstalled the OS, starting from the Software reinstall disk, and did all the upgrades to Tiger, and am still having the problem.
    My daughter didn't use Mail, as I didn't get around to setting up an account for her yet.
    I just used Sync to try to fix it, by importing all my settings, but still no go.

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