I'm having the same problem with my application.

Basically, it's a combination of jukebox/music management app I've been 
developing myself over the last few years. I had always used the dump 
commands to back up & restore the database, given that I develop on both 
linux and windows. When the backup commands were introduced, I switched 
them them. Things have been working fine.

General procedure is:
- backup database under windows, to my server
- reboot to linux
- restore from windows backup
- work
- backup database to my server
- reboot to windows
- restore
- work

and so on.
Until a week or so ago, both linux and windows were running 3.6.14. 
Recent upgrade of my gentoo system, however, upgraded sqlite there to 3.7.2

Now what I get is the following:

-backup database under windows to my server
- reboot to linux
- restore from windows backup
when I try to update or do anything in the database, my app crashes with 
the malformed database error.

If I nuke the linux database file, re-create from scratch instead of 
backup restore and load the virgin file from a dump, everything is ok.

On 2011-02-09 13:25, Dan Kennedy wrote:
>
>> I didn't find a way yet to reproduce the issue with a "clean" database.
>> Only way I can reproduce it is with some of the database, like the
>> test.db3. So I'm running out of ideas.
>
> This is the theory. test.db3 is an auto-vacuum database.
>
>     http://www.sqlite.org/src/info/89b8c9ac54
>
> Dan.
>
> _______________________________________________
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> sqlite-users@sqlite.org
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