Not unusual where code shares are concerned, it can be cheaper on the airline that actually operates the flight or it can be cheaper booking through the code share partner, which is where the search engines such as Kayak come in.
Be aware that if you book through a partner you may not get the tier/status miles in the FFP program which is worth considering if you need the points to maintain your current level or are close to moving up a notch. You should get the normal miles though.
The other day watched the screen at a departure gate as it cycled through nine different flight numbers and airlines sharing the same aircraft. I wonder if any two people on board actually paid the same price for their tickets.