Do these videos that don’t load properly in AE have any problems playing in video players on the same computer?
If so then there might be damaged codecs or codec conflicts on your system, which might be affecting separately what AE can encode and decode.
My first move would be to download and install the latest versions of all your codecs installed on your system, which is easy if you use codec packs such as K-lite for example (which I find quite comprehensive and stable – at least in Win7)
Graham Macfarlane
3D animator and VFX specialist
London UK