Hi Alexander,
It is difficult to solve a bug until the steps to produce it are known. As in the one you just solved, it is a little easier if it is actually happening for you, as it was not happening for me I had no idea where to begin to investigate the issue. In this case it was only affecting root level pages in other sites, because we were passing in the parentpageid, but for root level pages in all sites the parent id is -1 so it was affecting all root level pages in all sites when resorting root level pages, but it was not affecting child pages.
If you find any clues or a solution on this other bug I will fix it quickly.
Best,
Joe