Extra Inbox folder with 10.4 update

Old 10.4 upgrade issue still unresolved. With update, an extra Inbox folder was created under standard folders in list. ALL new mail goes there instead of standard Inbox. Only 1 POP account. Tried solution posted in this discussion earlier. Move "INBOX.mbox" from finder to desktop, restart Mail. Does not work: 1) On startup, extra Inbox is still there, and mail still appears in it. 2) Attempt to import mail from desktop folder into regular Inbox gives message "No Valid Mail for OSX was found."
I do run PocketMac Pro 3.5 to sync to an ipaq, but I have never selected mail as a sync option, only contacts and calendar. (wish there were another option here).
I tried the trial .Mac account and at one time had it posted to Mail before the update. Dropped it because of the problems syncing calendars. Not reliable at the time.
Can't think of any other variables that might be at work.
G4, dual 1.42, 1.5 gig RAM, multiple drives Mac OS X (10.4.3)

1. POP/INBOX.mbox/MESSAGES = " 0 kb"
2. Yes, I quit Mail. I made sure by shutting down and restarting the system as well.
3. I repaired permissions previously and did not see any references to MAIL folders of any kind. But I have done so again after another close of all programs, including Mail. Below is the report from Disk Utility:
Repairing permissions for “Tiger”
Determining correct file permissions.
We are using special permissions for the file or directory ./Library/Widgets/Dictionary.wdgt/Dictionary.js. New permissions are 33188
We are using special permissions for the file or directory ./Library/Widgets/Dictionary.wdgt/Dictionary.widgetplugin/Contents/Info.plist. New permissions are 33188
We are using special permissions for the file or directory ./Library/Widgets/Dictionary.wdgt/Dictionary.widgetplugin/Contents/MacOS/Dictio nary. New permissions are 33261
We are using special permissions for the file or directory ./Library/Widgets/Dictionary.wdgt/Dictionary.widgetplugin/Contents/version.plis t. New permissions are 33188
We are using special permissions for the file or directory ./Library/Widgets/Dictionary.wdgt/Info.plist. New permissions are 33188
We are using special permissions for the file or directory ./Library/Widgets/Dictionary.wdgt/version.plist. New permissions are 33188
We are using special permissions for the file or directory ./Library/Widgets/Flight Tracker.wdgt/FlightTracker.js. New permissions are 33188
We are using special permissions for the file or directory ./Library/Widgets/Flight Tracker.wdgt/FlightTrackerComboBoxPlugin.plugin/Contents/Info.plist. New permissions are 33188
We are using special permissions for the file or directory ./Library/Widgets/Flight Tracker.wdgt/FlightTrackerComboBoxPlugin.plugin/Contents/MacOS/FlightTrackerCom boBoxPlugin. New permissions are 33261
We are using special permissions for the file or directory ./Library/Widgets/Flight Tracker.wdgt/FlightTrackerComboBoxPlugin.plugin/Contents/version.plist. New permissions are 33188
We are using special permissions for the file or directory ./Library/Widgets/Flight Tracker.wdgt/Info.plist. New permissions are 33188
We are using special permissions for the file or directory ./Library/Widgets/Flight Tracker.wdgt/parser.js. New permissions are 33188
We are using special permissions for the file or directory ./Library/Widgets/Flight Tracker.wdgt/version.plist. New permissions are 33188
We are using special permissions for the file or directory ./Library/Widgets/Stickies.wdgt/Info.plist. New permissions are 33188
We are using special permissions for the file or directory ./Library/Widgets/Stickies.wdgt/Stickies.js. New permissions are 33188
We are using special permissions for the file or directory ./Library/Widgets/Stickies.wdgt/version.plist. New permissions are 33188
We are using special permissions for the file or directory ./Library/Widgets/Unit Converter.wdgt/Info.plist. New permissions are 33188
We are using special permissions for the file or directory ./Library/Widgets/Unit Converter.wdgt/UnitConverter.js. New permissions are 33188
We are using special permissions for the file or directory ./Library/Widgets/Unit Converter.wdgt/parser.js. New permissions are 33188
We are using special permissions for the file or directory ./Library/Widgets/Unit Converter.wdgt/version.plist. New permissions are 33188
We are using special permissions for the file or directory ./Library/Widgets. New permissions are 16877
We are using a special gid for the file or directory ./System/Library/CoreServices/Dock.app/Contents/MacOS/Dock. New gid is 0
We are using special permissions for the file or directory ./System/Library/CoreServices/Dock.app/Contents/MacOS/Dock. New permissions are 33261
We are using special permissions for the file or directory ./usr/lib/php/build/Makefile.global. New permissions are 33060
We are using special permissions for the file or directory ./usr/lib/php/build/acinclude.m4. New permissions are 33060
We are using special permissions for the file or directory ./usr/lib/php/build/mkdep.awk. New permissions are 33060
We are using special permissions for the file or directory ./usr/lib/php/build/phpize.m4. New permissions are 33060
We are using special permissions for the file or directory ./usr/lib/php/build/scanmakefilein.awk. New permissions are 33060
4. I will wait your instructions on renaming folders, etc. I do not have a huge volume of mail in any folder. I could transfer all of that mail into on the the "Personal Folders" to clean all of the other ones out if there would be a purpose or convenience in doing that.
Thanks again. By the way, I have Skype and iChat and a headphone set if you want to make an appointment and walk me through it.

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