Nevermind, it seems I have found the cause, I was doing:
                sqlthread->exec("PRAGMA synchronous = 0;",NULL,NULL);
                sqlthread->exec("PRAGMA cache_size = 4000;",NULL,NULL);

but changing it to this has sorted the problem out:
                sqlthread->exec("PRAGMA cache_size = 4000;",NULL,NULL);
                sqlthread->exec("PRAGMA synchronous = 0;",NULL,NULL);

It seems the value of synchronous gets changed back to full if you change
the cache_size.

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