Historical fare comes right out of US' fare rules regarding changes after travel has started. I believe this is there in order to prevent a fare recalculation from significantly increasing if a change made after the advance purchase deadline for that fare has passed. However, as mentioned, I don't often make changes so I could be misinterpreting this.
Besides that point, I believe two things have happened here.
1) The E-ACP was dropped from the recalculated fare. I can't find any documentation stating that this should have occurred.
2) The fare was recalculated incorrectly. One theory I have is that they added the tax twice. I too got $964.14 by adding up the new fare calculation segments (which is in CAD). If you convert it to USD with the ROE in the calculation I get $945.92. Add in the taxes and the total is $1057.79. That's eerily close to the CAD$1058.00 that they calculated pre-tax. It's almost as if they did the whole calculation manually, then entered it in the wrong field; the computer then exchanged it again and added the tax a second time.
I finally did get a response from the CP email; looks like they looked at it a little too quickly so I have sent it back for clarification. Otherwise I'll call the UK CP desk tomorrow. This will be fun to explain over the phone!