I have had several TATL flights with domestic segments and booked as various combinations of KLM, AF and DL flight numbers. Only domestic segments I get an upgrade on are those that are ticketed as DL flight numbers. I think AF flight numbers show up as upgrade eligible, but I'm usually way down on the list as a Plat. KLM shows as uneligible.

Have had similar issues with KLM not seeing Elite Plus status. Last trip the way over was KLM flight numbers and the way back was Delta. Outbound if I wanted an EC seat on the KLM segment (AMS-AUH) it was asking for full price, but was showing the Delta EC seats for free (ATL-AMS). On the return, was able to get KLM EC for 1/2 price as it should, Delta EC seat for free and got the domestic upgrade (at the gate and not at window).

My experince is that thigns are ugly and there is no good way to be sure to get your domestic upgrades, access to KLM EC benefits for the proper price etc. Using your ticket # on the AF / KLM sites does help for seat selection.