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Could it be that you are just using it wrong? You don't need the function selectPairs(), just use FREAK as the other descriptors, i.e. run your favorite detector and then use the compute() function of your freak-descriptor and you get a uchar-matrix containing the keypoint-corresponding feature vectors. See <your-opencv-folder>/samples/cpp/freak_demo.cpp for an example.
For the matching part you can then either use flann or bruteforce-matcher with Hamming-distance. Typically you don't use flann for tracking purposes since then you need to build an index each time, see also http://answers.opencv.org/question/17225/does-using-flann-matcher-for-every-frame-make/ for more thoughts on this topic.
