In CS6 I did a successful corner pin on one shot with the shot at normal speed/duration.
On the next shot I changed duration to 75% to lengthen it a bit and slow it down. Corner Pin would not work. It indicated where the moves would take place, but simply would not change the shape and do the effect.
Finally I realized if I rendered the the lengthened file first to a new file, then imported that file and put it on the line, then applied the Corner Pin effects, the Pin would work.