PHP 5.3.3 introduced sqlite3::busyTimeout(int milliseconds) which does not currently seem to be documented.
It believe it acts like sqlite::busyTimeout - that is it tells sqlite3 to call an internal busyHandler if SQLITE_BUSY is returned from any call which waits a short period and then retries. It continues to do this until milliseconds milliseconds have elapsed and then returns the SQLITE_BUSY status.
I don't know whether the default 60 second value is in place if this function is not called.