I have the same problem. Been digging around the internets for an hour or so and the best I can come up with is to save the Windows registry entry that tells IE the order of the bookarks, then restore it after Safari scrambles them. Here it is:
Yeah IE sucks just quit using it. I am baffdled by the amount of people who use IE 5 and 6 still. Such a tremendous security risk let alone the worst browsing experience ever. I mean I freak our when I can't open a new tab
No Regnad, I am strictly an IE user. I have no idea how Safari on the PC organizes bookmarks, although I was pleasantly surprised that Safari on the iPhone keeps the same order I put them in.