Hi Bill and thank you for answering.
Actually, my section access seems to be correctly configured but I use NTNAME instead of USERID and PASSWORD.
I use 2 QVW files for testing. One with Section Access like this:
LOAD * INLINE [ ACCESS, NTNAME USER, my_domain\MY_USER_NAME ];
And a second one with Section Access like this:
LOAD * INLINE [ ACCESS, NTNAME USER, MY_DOMAIN\MY_GROUP_NAME ];
These two files open nicely on local client (standard NT authentication) but only the first one opens when accessed through the server (with header authentication).
I think the problem migh be that you can't use your domain as a prefix to the username when using header authentication as QlikView will try validate the user against the AD which it can't because its simply receiving a username not pass through authentication. Try prefix the username with "CUSTOM\" instead which QlikView considers to be its own custom directory service.