There are a lot of good possibilities already listed. High ISO could easily make that much difference, if one camera has a lot of shots at high ISO vs. low ISO in the other camera. In addition I would ask, were both cards formatted the same way? For example: In camera. Also, are both cameras running the same firmware version?
As someone already asked, what happens when you switch the cards between the cameras? Maybe one of the cards has a bad area or lost files.
Do you have multiple cards in either camera? If one of the cameras is writing to both cards (SD and CF) and one of the cards is smaller, you will only have the capacity of the smaller of the two cards. If the camera is setup to automatically switch cards, it could be adding in the capacity of a second card in it's estimate, potentially showing a larger number of available shots.
There are a lot of possibilities, but when you say the settings are exactly the same, do you really mean all of the settings, or just basic settings like the exposure?
Assuming that everything else is truly set the same, then you could try formatting both cards in camera and see if the capacity varies, after formatting, before taking any pictures.