One possible reason for the database being locked that I ran into with SQLite is when I tried to access a row that was being written by one app, and read by another at the same time. You may want to set a busy timeout in your SQLite wrapper that will spin and wait for the database to become free (in the original c++ api the function is sqlite3_busy_timeout). I found that 300ms was sufficient in most cases.
But I doubt this is the problem, based on your post. Try other recommendations first.