How I solved issues with Mail.app and Spotlight

Even though my upgrade from Tiger 10.4.10 to Leopard was painless, the new OS X did have a few issues that had bothered me:
*Mail.app: * Every now and then, the app would behave like on its first startup, saying it needs to import my mail before I can work with it. What's more, at times I've had the phenomen that messages would appear empty on the preview pane and sometimes even when being opened.
*Spotlight: * Even though I let the indexing finish on the first day of working under Leopard, every now and then it seemed to start all over. First, I thought it's the NAS being indexed but it just went on to restart indexing each time I thought I had let it finish.
*Free disk space: * I tried to bring the usage of my homedirectory down so I would have enough free disk space to switch FileVault off and then back on so I could start using TimeMachine. But whatever I did, the free disk space just wouuldn't inrease - it just stayed the same (yes, I did let the system recover space on shutdown).
The *free disk space* issue made me think there was a problem with my disk but repeated runs with the Disk Utility yielded nothing...not for about a month. Yesterday I got some warnings about 'damaged but not repaired' but according to an Apple doc those could be safely ignored.
Somebody suggested to apply the combo update for 10.5.1 as that could solve some issues so I went ahead - after all, the update had already been applied earlier so just re-installing wouldn't hurt much, right?
Wrong.
The install of the combo update went smoothly, FileVault recovered some space on shutdown but upon restart I couldn't log in anymore: My homedirectory was damaged. The friendly OS X Leopard offered to repair it but soon later reported back that it failed doing so.
Now, to cut a long story short - deleting the affected user's account and using a different user on the same machine (without FileVault) solved any issues I've had. Mail now works like a charm (despite 40k+ messages with attachments), spotlight doesn't restart all it's indexing and disk space is shown correctly again. Also the odd corrupt file copy I had experienced occasionally (especially with large files) was gone.
My advise to anyone who didn't de-activate FileVault under Tiger to make the switch to Leopard: Even if you think it worked, switch it off and let Leopard set it up again. You may think things went right...but the above shows that there may be issues with it that you may blame other apps for...but they're probably not guilty at all.
I don't think the combo update actually caused FileVault to turn corrupt, it was just what broke the camel's neck. While it's no fun to lose your homedirectory, I'm glad the underlying issue finally came to light.

Thanks to this thread, it's been solved.
https://bbs.archlinux.org/viewtopic.php?id=97653

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