Ordering menu shuffles pages

After reordering pages with Nested Pages drag and drop, the pages are not always re-ordered. Happens with Menu Sync on and off. Sometimes, a few pages that were deep in the tree suddenly appear at the root on the front-end (but not in Nested Pages). I have to re-order them from WordPress > Appearance > Menus.

My setup:
– WordPress Multisite
– Polylang installed – but activated on one blog only and the bug is present on all blogs
– Around 100 pages on each blog
– Deepness: up to 4 levels