By Werner Ruotsalainen on Mon, 04/30/2012
UPDATE (08/20/2012): THIS post directly compares the remuxing speed of iVI and the, more or less (if you can live with the nagging screen upon loading a file and the disabled batch processing) free MP4tools. Very similar results to mine (read: iVI should NOT be used for MKV remuxing).
UPDATE (08/03/2012): HERE, I've elaborated on how iVI joins MP4 (MOV / M4V) videos without (!!) transcoding them; that is, very quickly.