Running the xunique command on a pbxproj for the first time resulted in a file that wasn't completely sorted. Running the xunique command again did not fix the sorting. However, after changing the order of any group in Xcode (by dragging a dropping) and running xunique again, the order of an unrelated build step was fixed. On another project, it took three times (modifying the project each time) to get the Xcode project appropriately sorted.