Mail: trouble with threads

I have been having some odd problems with Mail.app for the last day or so, and I haven't had luck finding anything online that seems to indicate similar problems. I'm running Tiger (10.4.6) on a Powermac G5.
I was fiddling with Mail last night, including adding a fourth account (gmail pop access) to check. I tried to change the icon on Mail, and the icon I mistakenly pasted in through the "Get Info" window was stuck there -- couldn't click on it to paste over it. Unable to find any similar problems online, I used Pacifist to reinstall Mail from my Tiger CD.
Since then, though, mail has been acting pretty wacky. When I click on threads to expand them, sometimes they expand, but usually they don't. I was able to uncheck "View Messages in Threads" (and thus get to my mail) in a couple mailboxes, but not in all. Often, when I switch mailboxes, the mailbox I switch into will appear empty and even say across the top, "0 messages, 1 unread." When I close the viewer window and open a new one, it will show all my messages again and correctly indicate, "32 messages, 1 unread." When I try to quit mail, it basically freezes up -- I can use the rest of my computer, but about a half hour passed after one time I told Mail to quit and Mail was still chugging along. It seems like if I can avoid clicking on threads, I can avoid these problems for the most part -- though, as I said, it won't always let me get out of thread view.
A few somewhat similar problems I read about online led people to suggest using Disk Utility to repair the hard disk. I tried doing that, and the things it listed highlighted in red/green included:
Incorrect number of thread records
Volume bitmap needs minor repair
Invalid free block count
Repairing volume
The volume Tanooki could not be repaired
Then it gave me an error message that said:
First Aid Failed
Disk Utility stopped repairing "Tanooki" because the following error was encountered:
The underlying task reported failure on exit.
Since then, I have also had trouble deleting mail. It often sits where it is, despite my attempts to delete, but it seems like it does find its way to the trash eventually; it just doesn't tell me right away, and sometimes I go back to find that it says it "hasn't been downloaded" (a problem normally associated with Panther to Tiger installs, I guess, though I did a full erase and install about a year ago).
There are so many variables above that I'm not even sure where to start. I've received advice elsewhere that I should be using Disk Warrior rather than Disk utility, but honestly, if the disk repair issue is less pressing than the issues with using Mail, it can wait. I appreciate any input you might have to offer. Thanks very much,
Jason
Powermac G5   Mac OS X (10.4.6)   Running Tiger about a year now

I used Pacifist to reinstall Mail from my Tiger CD.
Since then, though, mail has been acting pretty wacky.
Why am I not surprised? The version of Mac OS X on your Tiger install disks is probably earlier than the version you're using, which means Mail is probably out-of-sync with the rest of the system now.
A few somewhat similar problems I read about online
led people to suggest using Disk Utility to repair
the hard disk. I tried doing that,
You must repair whatever filesystem issues you have. If Disk Utility cannot repair them as described here:
The Repair functions of Disk Utility: what's it all about?
then read the "Disk Utility cannot repair the disk" section of the following article for additional guidance and links to more powerful (third-party, not free) disk utilities:
Resolving Disk, Permission, and Cache Corruption
The less you play with files until the issues are fixed, the better. After having fixed all filesystem issues, you should reinstall the Mail application using your Tiger installation disks as described here:
Custom installs in Mac OS X 10.4
If the version of the system software on your installation disks is earlier than what you're using now, then you must reinstall the appropriate system update afterwards, using the Combo installer, to bring the Mail application back in sync with the rest of the system:
Mac OS X 10.4.6 Combo Update for PPC
If you had installed a Security Update meant for the version of Mac OS X you're using, you'll have to reinstall it as well:
Security Update 2006-003 Mac OS X 10.4.6 Client (PPC)
if the disk repair issue is less pressing
than the issues with using Mail, it can wait.
You cannot wait. You must repair the filesystem issues before trying to fix anything else.

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