Mail messages missing after upgrade to 10.4.3

Short story: I upgraded a Mac from 10.3.9 to 10.4.3 and now none of my old received mail messages are in my inbox.
Long story: Installed Tiger using "Archive and install". Repaired permissions. Installed the combo updater to 10.4.3 using software update. Repaired permissions again. After the system was upgraded to 10.4.3 I opened mail. It said it was importing messages. However, when it was done, there were only 6 messages from the last few days. The other 400 or so messages that had been in mail (in the inbox) in the previous version were not in the mailbox. I tried rebuilding the mailbox. This resulted in losing all of these 6 messages. I tried importing from the old account mailbox and mail re-created the mailbox structure, again with only 6 messages in the inbox.
I have tried re-importing my inbox which is listed as 18.2 mb in size but I get a dialog box that says there are no valid mail messages to be imported. I have tried importing messages from my backup disk, a backup created before the 10.4.3 upgrade but it gives me the same “no valid messages to be imported.” I have tried rebooting but there are still only 6 messages in the inbox to be seen.
Of note, the sent mail box is full of messages and appears to have been upgraded appropriately.
The application mail and all associated mailboxes etc are in their default locations. I have not moved or modified any of the locations of files.
Any ideas on what happened and more importantly how to restore or otherwise make visible all of my mail messages?
Thanks,
Pete

Hi Ernie! I really appreciate your assistance. Are you ready for this? I had 13 POP accounts... Here is the current info on the files on my Mac (upgraded from 10.3.9 to 10.4.3 last night)
Pop Account 1 Folder (Main email account lost all inbox messages)
INBOX.mbox contains:
- content_index (3.9 MB)
- content_index-h-67-100-128-207.sttnwaho.dynamic.covad.net-542 (5.3MB)
- Info.plist (4KB)
- mbox (117.1 MB)
- Messages (empty folder)
- Messages-T0x560b9f0-pyksdq (contains file named 1.emix, 4KB)
- tableofcontents (264 KB)
Pop Account 2 Folder (Smaller email account appears to be intact)
INBOX.mbox contains:
- content_index (208 KB)
- Info.plist (4KB)
- mbox (416 KB)
- Messages (Folder contains 31 "emix" files, 488 KB)
- tableofcontents (8 KB)
Pop Account 3 Folder (Minor email account - not much was here, might be ok)
INBOX.mbox contains:
- content_index (16 kB)
- content_index-h-67-100-128-207.sttnwaho.dynamic.covad.net-542 (8 KB)
- Info.plist (4 KB)
- mbox (4 KB)
- Messages (Folder contains 1 "emix" file, 4KB)
- tableofcontents (4 KB)
Pop Account 4 Folder (important email account lost all inbox messages)
INBOX.mbox contains:
- content_index (1.4 MB)
- content_index-h-66-167-49-109.sttnwaho.dynamic.covad.net-455 (1.4 MB)
- Info.plist (4KB)
- mbox (3.3 MB)
- Messages (empty folder)
- Messages-T0x560b9f0-4voERb (contains 1 "emix" file, 4KB)
- tableofcontents (40 KB)
Pop Account 5 Folder (Minor email account - couple messages made it)
INBOX.mbox contains:
- content_index (20 kB)
- Info.plist (4 KB)
- mbox (8 KB)
- Messages (Folder contains 2 "emix" files, 12 KB)
- tableofcontents (4 KB)
Pop Account 6 Folder (Minor email account - couple messages made it)
INBOX.mbox contains:
- content_index (8 kB)
- Info.plist (4 KB)
- mbox (4 KB)
- Messages (Folder contains 1 "emix" file, 4 KB)
- tableofcontents (4 KB)
Pop Account 7 Folder (important email account - inbox seemed to come through - not positive it is all there, but it looks good)
INBOX.mbox contains:
- content_index (2.8 MB)
- content_index-localhost-574 (2 MB)
- Info.plist (4KB)
- mbox (25.9 MB)
- Messages (Folder contains 670 "emix" files, 25.9 MB)
- tableofcontents (176 KB)
Pop Account 8 Folder (inbox messages appearing - not sure they are all there)
INBOX.mbox contains:
- content_index (628 MB)
- Info.plist (4KB)
- mbox (2.7 MB)
- Messages (Folder contains 130 "emix" files, 2.9 MB)
- tableofcontents (28 KB)
Pop Account 9 Folder (Minor email account - couple messages made it)
INBOX.mbox contains:
- content_index (116 KB)
- Info.plist (4 KB)
- mbox (1.9 KB)
- Messages (Folder contains 4 "emix" files, 1.7MB)
- tableofcontents (8 KB)
Pop Account 10 Folder (Smaller email account appears to be intact)
INBOX.mbox contains:
- content_index (16 KB)
- Info.plist (4KB)
- mbox (12 KB)
- Messages (Folder contains 4 "emix" files, 20 KB)
- tableofcontents (4 KB)
Pop Account 11 Folder (inbox messages appearing - not sure they are all there)
INBOX.mbox contains:
- content_index (756 MB)
- Info.plist (4KB)
- mbox (13.6 MB)
- Messages (Folder contains 152 "emix" files, 12.3 MB)
- tableofcontents (60 KB)
Pop Account 12 Folder (inbox messages appearing - not sure they are all there)
INBOX.mbox contains:
- content_index (500 MB)
- Info.plist (4KB)
- mbox (5.7 MB)
- Messages (Folder contains 93 "emix" files, 5.5 MB)
- tableofcontents (24 KB)
Pop Account 13 Folder (inbox messages appearing - not sure they are all there)
INBOX.mbox contains:
- content_index (80 MB)
- Info.plist (4KB)
- mbox (128 KB)
- Messages (Folder contains 13 "emix" files, 148 KB)
- tableofcontents (4 KB)
When I compare the above INBOX.mbox files to the 13 POP account folders in my pre-upgrade Retrospect Backup, the files sizes match, but the difference is there are no "Messages" folders in the backup - I assume these are folders/files Tiger built (and screwed up) during my first launch/import of the Upgraded Mail.
Thanks again for looking at this.
Mary

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