On 5 Oct 2016, at 11:37am, Daniel Polski <dan...@agelektronik.se> wrote:

>> Do your applications use any PRAGMAs ?
> PRAGMA foreign_keys=ON;
> PRAGMA journal_mode=WAL;

Both of those should be safe in this context.  It's not normally necessary to 
set the journal_mode each time you open the file.  It's stored inside the file 
and SQLite automatically sees it when it opens the file.  You might want it if 
you are creating a new file each time, though.

>> Are they running on the same computer both accessing storage held on that 
>> same computer ?
> 
> It's different threads within the same application. Threads have "own" sqlite 
> connections.

That should be safe too.  I hope someone else can help debug your problem.  
Many bugs like the one you mentioned are a result of

a) having other parts of your program misuse SQLite file handles
b) having other parts of your program overwrite memory SQLite is using
c) using file storage mounted across a network with buggy network systems

Maybe that will help.

Simon.
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