I have seen a couple of complaints about this, and I was having the same trouble myself. This morning I figured out what must be going on—-the Trenitalia website is changing the time of travel based on the time zone you are in. In my case, they are adding 9 hours to the desired departure time I enter in my search.
You can read more about this, and see the solution on this thread:
apparently the Trenitalia app does not have this issue.