Why would US, UA and AC necessarily charge the same price. This sometimes happens, but usually doesn't. When i book my flights, I always check UA and AC, and occasionally, they are the same, a lot of the time, there is an about $20 - $40 difference, and sometimes, it can be hundreds of dollars difference for the same flight. As an example, once I looked up a flight, and was $400 or so on united.com, and $750+ on aircanada.com.

Back to the OP's question, I think the base fares are different because of a few things, noteably the currency you are booking in. Believe even if you are booking on the Canadian version of AC.com, the base price is listed in US dollars, then converted if you are booking a flight ex-US. Also, I think there are different laws governing what taxes have to be included in the base fare in each country. I know I used to check both Canadian and US versions for my EWR-YYZ trips, and often, the final price was the same, but the base price would be very different.