Mail messages disappear from the Inbox, but are still in ~/Library/Mail

Question

Folks,
I'm encountering a perplexing problem on my parent's eMac; any input would be very much appreciated...here's the story:
Over the weekend, I upgraded my Dad's 1.25GHz eMac G4 to Tiger (it had been running 10.3.9). The upgrade went smoothly, and all seemed well. I applied all the latest Apple Software Updates to get the eMac to 10.4.6, and once again, all seemed well. I performed the usual Disk Utility "permission fixing," as well, and nothing came up that seemed unusual. I did notice that I encountered the "spinning beach ball" a fair amount during routine operations, but I attributed this to the fact that the eMac only has 512MB of RAM (it's going to receive another 512 in a few days), and that I was just being impatient, given that I am accustomed to my own machine, which is a relatively snappy dual 2.5GHz G5 with the full complement of 8GB of RAM. A day or so later, Dad reported that the Mail app was not starting; upon clicking the Mail icon, it simply bounced several times, and then simply stopped bouncing. I looked at the crash logs and found that Mail could not locate a needed file/library located in /System/Library/Frameworks/SyncServices.framework. In addition, I noticed that the iCal app and the Address Book app were also crashing (the icons of each would bounce, just like Mail's, then stop, without the apps actually firing up). The crash logs revealed that those apps were also looking for this mysterious file, which apparently had somehow been misplaced/lost. I used the "Pacifist" program to reinstall the contents of that particular directory (using the Tiger install CD). Much to my relief, once that directory was reinstalled, the apps once again started up and worked normally. HOWEVER, I noticed some odd behavior with the Mail app. The first thing that became evident was that the Inbox did not show all the messages that had been there before. Looking under the ~/Library/Mail/POP-Dad's account/INBOX.mbox/Messages directory, however, it was clear that all the messages were indeed there (in the form of the individual .emlx files). They just did not seem to be displayed in the Inbox of the Mail app. I tried doing a "rebuild" of the mailbox, but this did not result in any additional messages being displayed. Any thoughts?
The other perplexing behavior is this: the Mail app on the eMac can send and receive mail, but, once you click on a newly-received (unread) message, and then go to another mail box (say, for example, the "Drafts" or "Sent" folders), and then return to the Inbox, the message that was just received is no longer displayed/listed in the Inbox. Once again, looking in the ~/Library/Mail/POP-Dad's account/INBOX.mbox/Messages directory reveals that the message IS there (again, in its own .emlx file), but is simply not being displayed in the Inbox. I can click on the individual .emlx files, and they open new windows in Mail, from which you can hit "reply" or "forward," as normal; it just won't display the actual message that was originally in the Inbox. Sent messages, however, seem to be saved/displayed normally.
I've searched through the Mail discussion forum, and while I've found discussions along generally similar lines, I have not located an entry dealing with these particular symptoms. As such, any input/suggestions would be greatly appreciated.
Thanks in advance for your time.
-Javier

Answer 1

Regarding the missing package that you reinstalled with Pacifist, it would have been better to fix the problem by reinstalling the Mac OS X 10.4.6 Combo Update. Actually, you're going to have to do that anyway, as the package you installed came from an older version of Mac OS X and could now be out-of-sync with the rest of the system. Not only that, but if there was something amiss with that package, chances are that something else went awry as well, so you should really reinstall the latest Combo Update. Read the following articles for guidelines on how to properly install system updates:
Troubleshooting installation and software updates
Installing software updates
Basically, you should verify/repair the boot volume (not just permissions) before installing the update, and no applications should be running while installing it.
As to the missing messages, the conversion from Mail 1.x to Mail 2.0 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."
If you see a strangely named Messages-XXXXXX folder within any of the *.mbox folders in the Finder, that means the conversion didn't proceed as it should, so be careful about deleting the old files, as they may contain messages that didn't come through. Better just move them out of there if you wish.
I partially disagree with Allan (and with Ernie, who also has troubleshooted a lot of similar cases and believes the old files could still be troublesome after a successful conversion as well) in that I don't think the problem with Mail 2.0 is the presence of the old files, but rather that, as a result of the improper conversion, there is something wrong with Envelope Index and with some of the converted messages themselves. IMO, the old files shouldn't be a problem if the conversion worked properly. Mail should just ignore those files when it sees a proper Messages folder in the mailbox folder.
The reason you cannot see in Mail some messages for which an *.emlx file exists is precisely that there is something wrong with Envelope Index. Mail will simply ignore any *.emlx file for which a corresponding entry does not exist in Envelope Index. Actually, Mail doesn't look into the Messages folder at all when displaying the mailbox contents, it just loads whatever there is in Envelope Index. If that information is wrong, the information displayed by Mail will be wrong as well; it may refer to messages that no longer exist, ignore messages that do exist, display one message but load a different one when you open it, etc.
Re-creating Envelope Index without cleaning up the mailboxes first would probably fail and it could even make things worse, though. That's what makes troubleshooting these issues harder than it should be.