I had the same problem after I upgraded to wordpress 2.84, and then subsequently updating to the latest nextgen. But I managed to solve this by going to Nextgen Gallery’s Options -> Gallery, and I re-selected Sort Order as ‘custom’, and saved the changes. And this solved it. I suspect that an upgrade of the database that was required after an upgrade of NGG did not copy over the ‘Sort Order’ value properly. Or maybe a different fieldname was used to store the ‘Sort Order’ value in the updated db – Have yet to verify.
