You need to not dismiss the possibility that you are doing something wrong. Review Rip's low-bar position video (in the videos section). Post a pic of where you are putting the bar. See a coach, if necessary. I doubt desk jockey = so inflexible that you can't attain the correct position, since I am one.
As far as stretching goes, just do the low bar stretch, as recommended in the video, each time you squat. All else being correct, this will sort itself out in a few weeks.