Long runtimes for Quartus II

I can tell you, from experience, the routing phase is running when the fitter progress bar is at 79%. Although it appears that the progress bar is "stuck", there is often a longer lag time at that particular % than other numbers. You may want to take a look at a message the prints out the routing interconnect utilization (both average & peak) to see if there is a noticeable difference between the two flows you are using. Also, you should take a quick look at the fitter report file to see if the design compiler used a different set of settings than the ones used in approach A.