Kenny from ACF support was able to sort this out for me quite easily, here is his response;
I suspect that the issue affects your current user because you had “reordered” metaboxes on the edit screen.
The “fix” we added on the latest version, changes all “high” metaboxes to “normal”. This allows metaboxes to appear correctly in Gutenberg, but is most likely conflicting with your users “reorder” setting.
To change and fix this from your end, please edit the wp_usermeta table and delete the rows containing “meta-box-order_…”. This will allow all metaboxes to appear as expected.
Basically I just removed all the “meta-box-order_*” entries from the wp_usermeta table in the database and now I can see everything as normal again.