Sometimes, the availability of room types is the reason for price discrepancies. If the lowest-level room type is not available all nights, the website will default to the next level. For example, some hotels might charge an extra $10 for a room with two beds. That difference might be easy to miss, as the room category (standard or club) is what most people notice.
So, if booking a multi-night stay using multiple reservations, be certain to check the room types.