Vault Issues

Hi,
Like many people on this board I'm having some problems with the vault. Like many, I have the issue of Aperture quitting when I click the show vault icon or the update icon in the bottom left of the Aperture window.
However, my workaround for this is that if I select the "view vaults" icon when no drive is connected the pane appears, THEN I plug in my firewire drive and everything seems to work fine.
MY PROBLEM(S):
1. My vaults do not seem to do incremental backups. Everytime I hit update vault it takes approx 3-4hrs to update. My library is 140GB. This leads me to believe that it's not doing an incremental update.
2. I usually get an error message that informs me that ONE small file deep in my library, a "Version 1" was not able to be created. This is usually a 8-32k file and I can just drill down in the package contents of my library and using drag and drop, replace this one small file manually in the package contents of the vault.
However, after this two step process (1. replacing the whole vault everytime, and 2. the error message) Aperture indicates that I still need to do an update. It indicates that the same number of projects and images need to be updated on the splash screen AND the vault update icon is still red (BTW, I've NEVER had my icon appear yellow. It only seems to come in red or gray/black).
Moreover, when I look at the vault in the finder it indicates the last update was, in this case, 10/13/08. NOT today 12/16/08.
So that's the whole mess....
Any advice would be greatly appreciated.
THANKS!

Tony,
Thanks very much for your help. What has happened to me has happened before. I back up to vault once and I always get the same error message. Then I do it again and all works fine. Which is what happened yesterday.
I did throw out some thumbnails at the finder level and Aperture rebuilt those. I don't know if that's the problem.
You make TWO VERY GOOD POINTS re: rebuild library and vault format.
I have considered rebuilding the vault, but have read some real horror stories that have prevented me from going through with it. Same for consistency check.
Would you happen to know if rebuilding large libraries improves responsiveness of Aperture? I've read that it has. In other words, is it good routine maintenance or is it just for when you get into trouble?
With regard to vault format: That may be my problem. I'm using a WD 500gig "My Book" firewire as my vault and unlike other external drives I have, on this one I forgot to format it out of the box. As such it is MS-DOS (FAT32) formatted. Of course that means throwing everything off that drive, vault in included, and starting again. However, if you feel confident that that needs to be done, I'll do it.
Thanks for your help
Christian

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