Are you doing any actual work that requires the data in the datastore to be saved? Or is that a temporary storage location while you process the data to populate other tables? Are you running SQL queries against the stored data that could be turned into datawindow computes?
Can you give us an idea of what type of processing you're doing with the text file data once it's parsed and in the datastore? That may give us an idea of what part of the process may be slowing it down.
Have you done logging within your code to see exactly where it's getting slowed down? Writing a text file with a timestamp and tag output can be really helpful in seeing how a system runs in the real world.