I'm working on several projects that use Canon mxf files in AE CS6 and everything worked just fine. Yesterday I installed the newest update and now it tells me they are unsoppurted or corrupted. I also switched from the trial to a paid version (but I dont think thats too important)
32gigs of Ram
nvidia quadro 2000D
After Effects 18.104.22.168
Edit: If i dynamic link from premiere, its all ok, but i enjoy having my AE projects be standalone...