I’ve just noticed this issue. I created two field groups and assigned them to options page(site settings). Then i reordered them using drag-and-drop functionality and clicked “Update” button. After page reload i can see the order didn’t change.
Then i tested reordering on page and post and it worked like a charm.
So it’s look like field groups reordering doesn’t work only on options page.
To reproduce issue:
1) create new wordpress site
2) install latest version of acf pro(6.3.11 for this moment)
p.s. also group toggling doesn’t get remembered after reload on options page