I've also been struggling with this on my Ipad 3 / Windows 7. I performed a test where I created a folder and copied 2 photos into it, an old one and a new one. I renamed the old file to 1111 and the new file to 0000, so the new file would sort first if it was by name, or last if it was by date.
The first time I synced, the files showed up in name order, but the next time I synced, they changed to date order.
So there's is something strange definitely going on, and it's not even consistent between syncs. My suspicion is that on the first sync the files are dicovered and added in name order, but then the exif or file date data is read into the database, and then on the next sync that is applied.
The solution may be to have all the dates and names in the correct order, so there are no conflicts between them.