What type of queries are slower, e.g. SELECT, INSERT, UPDATE, DELETE, etc?
We observed only in SELECT Statements when the column is not indexed.

Are you using the connection pool?
We dont use the connection Pool. We just use the normal SQLiteConnection.

How many threads are accessing the database?

Ours is a multithreaded and mult-processes application. However, we were able to reproduce the issue with a single-threaded test application. So it occurs in all cases.