Even running a repair will not restore files that are there but are not made right. The only way to fix what has happened is to do one of 2 things, uninstall and completely reinstall FSX which will restore the original files, or install a light fix that works right. The only one I know of that will work for sure to get rid of the blocks is this one:
http://www.simviation.com/cgi-bin/syb.cgi?section=misc&file=Nicks_Lightfix_V2.zi... but those are not made for FSX and the timing is off because of that. But the textures in it will get rid of the blocks because they are made right.
I dont know if your problem is textures or fx files or both.
Nicks light fix was made for FS9 so you will have to install the files to a separate folder and then manually browse to there and move them where they belong in FSX. Just copy/past the Effects and the Texture folders into the FSX install folder and let it over-write the orginals. The folder and file names are the same but the install folder is different.
you could just try manually moving the textures and not the FX files into FSX from that package and see if they work. Nick has been in the process of writing an entire new light package for FSX right now
http://www.simviation.com/cgi-bin/yabb2/YaBB.pl?num=1189390905