Why are the backs in reverse order?
Because you flip the stack. The last sheet ends up on top, so the scanner reads back 10, back 9, back 8 … while the fronts were 1, 2, 3. Interleaving without reversing gives you front 1, back 10, front 2, back 9 — a document that reads as nonsense.
The same applies to phone scanning apps if you photograph one side of the pile and then the other.
What if the backs are upside down?
Common with a flipped stack: every even page is rotated 180°. Open the interleaved file in Organize PDF Pages, select the even pages and rotate them together, then save. The rotation is stored in the page, so it is right in every reader and when printed.
Do this after interleaving, not before — it is one pass over one file instead of two.
What about blank backs?
Sheets printed on one side leave blank pages every other page. Delete them in Organize PDF Pages once, rather than trying to scan around them; the thumbnails make blanks easy to spot.
If the scanner has a blank-page detection setting, it may have dropped some already — which breaks the strict alternation, so check the pairing before deleting anything.