UPDATE:

That "more information that may tend to confirm" did surface, and it does help confirm the story.

But first:

Now, Amtrak has now admitted it. It may be because they were prodded into telling the truth by having parts of the story ("train may have run early") posted to a discussion forum (*wink*).

A new train status entry for Train 4(5) at Flagstaff is now appearing. Previously there was no entry at all, either arrival or departure.

Now there is an arrival time at Flagstaff. The train arrived Flagstaff at 446am, before it was supposed to depart Williams Jct., 30 miles away.

* NDL * * 2 1223A * 1239A Departed: 16 minutes late.
* KNG * * 2 223A 2 233A 245A 250A Departed: 17 minutes late.
* WMJ * * 2 450A (no actual times posted) MST
* FLG * * 2 536A 2 541A 446A Arrived: 50 minutes early.
* WLO * * 2 639A * 642A Departed: 3 minutes late.

This confirms that the train actually ran way too early at Williams Jct., and arrived early at Flagstaff, although nobody has yet changed the times at Kingman. But did it also depart Flagstaff early?

That "more information?"

We have found out that Train 4(5) was delayed between Flagstaff and Winslow because of freight train interference (as rare as that magnitude of delay is on the BNSF Transcon, that's what is being claimed). It was held at two places for a total of 42 minutes. If it had actually departed Flagstaff at the scheduled time and arrived at Winslow as claimed, after sitting still for 42 minutes, it would have traveled 58 miles in 17 minutes.

If that happened, the possibilities are that the Southwest Chief is a time-travel machine; or that true High Speed Rail has arrived at last; at 208mph, who needs Acela?

I think we know it really departed from Flagstaff substantially early.