Check the Live update better, to see if you have some warnings.
If there's a syntax error in the prepar3d.cfg file (usually because having edited it by hand), the updater will default to using MSAA, because it will never try to write on a corrupted/illegal file.
Also, if you have both P3D V4 and V5 installed, if any of the two has MSAA
so most textures examples in Basel will flickering in V5.
I'm sorry but, this cannot simply happen, unless you meant the opposite of what you said, that you had MSAA enabled in the sim, and the update is installing the SSAA version of the textures.
The issue is, the SSAA version of the textures are those that might flicker if you have MSAA enabled in the sim. Flickering is caused by MSAA not handling normal maps very well so, the difference between the two texture sets is the MSAA version has normal maps almost entirely flattened, so they won't flicker with either setting.
