The parsing routine seems to fail to read correct entries within the cfg file. All what found within this cfg file is what set by the P3D UI.
The parsing routine works correctly. I think I understood what happens in your case. Do you also have P3D V4 installed, and that is set to MSAA perhaps ?
The issue is, this detection is made to decide which set of textures to make active, and since the FSDT installation is shared, it's not possible to have a different set of textures installed for P3D4 and P3D5.
What the updater does, is first check P3D V4 ( if it's installed ) and, if it finds you have MSAA active there, it's stop looking for P3D V5 as well, since even if you had P3D V5 set for SSAA, it wouldn't be possible to have both sets active so, again, under the same reasoning of err on the safe side, it chose to go with MSAA textures.
So, if you want to install SSAA textures automatically, you must set SSAA in P3D V4 as well.