Cursor (waveform) reading not the same with transcript window
That looks correct.  The values in the transcript window are the signal levels 'leading in' to the clock edge.  This constitutes an ideal setup time.  With the cursor positioned directly on a clock edge, the values to the left side will be the 'inputs' and the values to the right side will be the 'outputs'.  This represents an ideal propagation delay of zero, setup time of one clock period, and hold time of zero.  You will have to delay the input by the propagation delay of the logic (in this case one clock cycle) if you have to directly compare it with the registered output.