Wrong fundamental matrix results

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Opencv's findFundamentalMat gives different results from the one returned by stereoCalibrate, on the same points (10 checkerboards worth of points concatenated in a long vector). The resulting translation matrix (SVD of E) is wrong when accounting for scale.

I tried both FM_RANSAC and FM_LMEDS. The second one one gives better results in some cases, but in most they are both wrong. Is there some kind of restriction on the points that are given to the function (i.e. they should not be coplanar, which the checkerboard corners are)?