There's an important distinction between leaving the US temporarily, and leaving permanently, which is as much as anything dictated by you returning to your place of residence.
If you are in the US under the Visa Waiver Program (VWP) and you leave the US for a few weeks to visit Canada (or Mexico) with an intent to return to the US then you are deemed to have only temporarily left the US for that period, and thus your 90 days carries through - even though you're out of the country. In the days of the I-94W forms (the green form you used to fill in when arriving in the US), you would actually keep your I-94W in your passport even when you left the US.
If you are leaving US to return to your place of residence, then you are leaving permanently. In this case your VWP period would end when you left the country, and historically that's when you would have turned in your I-94W.
As you have a work visa to be in Canada, for the period of that visa Canada would be your place of residence. That means that every time you leave the US your visit will have deemed to have ended as you've returned to your place of residence, and thus permanently left the US - which means that when you re-enter the US the VWP clock will be restarted.
At the end of the day the Canada/Mexico condition is intended to stop people doing visa runs from the US to Canada/Mexico, thus getting another 90 days on their VWP. If it's clear that's not what you're doing then you'll have no issues.
Don't forget that to enter the US under the VWP you will first need to obtain an ESTA.
(Note: Usual provisions apply. IANAL, but I've entered the US around 40 times both on VWP and on Visas so I know the processes fairly well! If you want a definite answer, either contact USCIS, or talk to a qualified immigration lawyer)