Delay in sqlite query execution

We have big network of client system running with sqlite database under Debian6 (kernel 2.6.26-1-686). The sqlite version running is 3.7.3

The client frequently will perform query based actions. out of these actions 30% query execution having delay in it's execution. (Note that we are using thread safe query execution. So SQLITE_BUSY is not received).

For example, sometimes the UPDATE command executed in fraction of second and in sometimes it takes 3 to 10 seconds.

If there anything related to Sqlite version or the hardware usage?

Pl root us to identify the cause.

Thanks!