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I've found the following issue on bug tracker: SURF : different number of keypoints between OpenCV 2.3 & 2.4 (Bug #1911)
It seems that there are some differences in SURF feature detector in OpenCV 2.4. One change is that extended parameter is set to true by default, so descriptor length is 128 not 64. Also it seems that in 2.4 more keypoints are located - but if this is for purpose or is some error/bug is not clear yet.
See: http://code.opencv.org/issues/1911
