ENBSeries

When I start skyrim, I get the red line of text "hardware aa detected" but as far as I can tell none is on. I reinstalled about a week ago as I tried to fix various video-related issues I was having. Also, I use "mod organizer" which keeps the skyrim dir clean.

skyrim launcher has both HWAA and FXAA to off and the nvidia control panel is set like so.
http://imgur.com/zRFct80
http://imgur.com/yBEi4dl

End result is that sometimes I get the warning, sometimes not, and I still have anomalies related to hwaa being on.
[edit] i discovered that it shows everytime, except sometimes it will wait till I change cells.

enb disabled: http://imgur.com/inlnx9B
enb enabled: http://imgur.com/wvWKDY7

The body isn't like this everywhere, but static meshes pop in and out in random places when enb enabled. This wasn't a problem at all until I upgraded enbseries to 217

the questions are:
In the nvidia cpanel, is it better to set these things to OFF or "Application controlled?"
Where else can I check to make sure hwaa is off?
What could be causing the problem with meshes?

"Application controlled" - valid value for antialiasing options. And that red message appear only when aa enabed, so whatever you say, it's fact. Try to restore skyrimprefs.ini and skyrim.ini and don't use that damn mod organizer, it may create another copy of ini files.

I forgot that mod organizer virtualizes a lot of things, and I hadn't fixed the skyrimprefs.ini that it uses. Once i set "iMultiSample=0", now it works, including the SSAO problem I had.

for managing the > 40 mods I use (of all kinds) it would be impossible to play the game not using mod organizer. I can't imagine dealing with it manually or with nmm. Load order alone makes it worth it.

So my game works now and I will continue to use it.

Instead of Mod Organizer, you could use BOSS. As far as I know it does not tamper with your inis, only load order.