Import Mail working partially

I've browsed through an enormous amount of these posts looking for my issue but have only found partial fixes. (One of the previous questions solved an unrelated issue, so that was a relief). But here is the current problem.
After getting my PowerBook back from AppleCare (new hard drive), I began to start moving all of my previously-backed-up data onto the laptop. iCal, Address Book, iLife apps, all that was going well. But Mail is giving me trouble.
I was able to import most of my mail that was backed up, but some of it refuses to come back. From looking at the folder of messages, there should be hundreds and hundreds of emails getting imported from two specific and important folders (Inbox & Sent). However, only 14 emails are being imported total. The .mbox file extension is correct (it is a POP email account that only stores files for a temporary time on the server, so the rest of these that I have must be manually input) but most of these emails are nowhere to be found.
If anyone has ideas or suggestions, I would really appreciate it.
PowerBook G4 12 1.5GHz   Mac OS X (10.4.4)  

I can't answer, but have had the same problem. In my case, it was a mailbox that I inadvertently deleted and pulled out of a backup, so there shouldn't have been any data corruption. I only mention this because some people may write off your problem as corruption in the rescued data, but my mailbox also was supposedly placed into an Import folder, which doesn't actually exist anywhere that I can find. (Even in the ~/Library/Mail/ folder anywhere.)

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    At this point, whether you go back to Mac OS X 10.3 and tidy up your mailboxes there (if that’s still an option), or want to try to fix the problem in place using the procedure I’ll post below again for reference, is up to you. Do what you find easier or more convenient. Whatever you do, be sure you keep a backup of the original ~/Library/Mail folder, so that you can try something else if things don’t work as expected.
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    The Repair functions of Disk Utility: what's it all about?
    For a POP account, the following procedure should allow you to fix the Inbox problem. A similar procedure should allow you to fix other mailboxes that might also be affected:
    1. Quit Mail if it’s running.
    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/.
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    6. Move any strangely-named Messages-T0x... folders 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.
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    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.
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    If all is well and you don’t miss anything, the files on the Desktop can be deleted, although you may want to keep them for a while, just in case.
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    Overstuffed mailbox is unexpectedly empty
    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. That is, ~/Library is the Library folder within the user’s home folder, i.e. /Users/username/Library.

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