This actually happened to me two days ago - was booking an itinerary that priced on ITA and Expedia as $320ish but on Delta.com and Orbitz as $335ish. Same fare class, T, same fare basis code, TA14A0NJ, same exact routing.

I was booking right on the 14 day advance purchase boundary, so I figured it was a timezone difference or something at the time...

I took a ton of screenshots on Expedia and then proceeded to book on Delta.com (as I there was a chance I might need to use the 24 hour cancellation policy). When I clicked through the summary page to try and purchase, Delta.com siad "the price of your itinerary has changed, and is now $320. Is this OK?"

So if you encounter discrepancies in the future, you may consider clicking through one level beyond the summary page to see if the pricing engine fixes its mistake...