how do these travel websites work?

I spent the majority of the day yesterday trying to book a flight for Shel to go to Wisconsin on very short notice. Travelocity, Expedia, Cheaptickets, Westejet, Sears travel, you name it, I tried it.
At one point I got on the phone with my sister in law in the USA. I was on a site and having difficulty with payment and asked if she could help me. She went to the same site, we logged on and entered travel details identically and her site brought up tickets for about 400 dollars cheaper than my site did. This was for the same person, starting and ending in the same place on the same dates of travel. I simply don't understand how it is possible for this to happen. She tried to pay from her end because I was having difficulties from my end. We were getting the same error message as we tried to pay with a credit card.
We called the bank and verified the credit card info AND the fact that the charges for the credit card had come into the bank every single time we entered them on the site. That took a bit of clearing up to do because between her and I and our mutual obsessiveness we had tried to enter credit card information a number of times each. Once that was cleared up the bank advised us to call the website. The website advised us to call the airline. The airline said the problem was with the bank.
Needless to say we exited that site!
At the end of a gruelling day online trying to get Shel to Wisconsin as early as we possibly could, we ended up buying the ticket from the USA, paying Canadian funds for the ticket, but getting almost a thousand dollars off the price as it was listed where I was accessing the site in Canada. Strange.
I POSSIBLY could comprehend if the sites were different - in the way that amazon.ca is different from amazon.com, but these were IDENTICAL sites being browsed simultaneously. In any case, with MUCH appreciation for her sister and the time she spent getting flights booked, Shel will be on her way in just a few days, and for a few hundred dollars cheaper than I was able to find.