The MOV files are encoded with the PNG codec. Some systems are not natively configured to read the PNG codec and will show an error or replace the alpha channel with black. There are a few ways to get the codec loaded in your environment, you can install the latest version of Quicktime (or update it if you already have it), or you can install the k-lite codec pack on windows or Perian on mac. ( Also the newest version of AE already has the PNG codec built in. )
The other option is to use a video transcoder such as Handbrake or MPEG Streamclip to convert the files to another format supporting the alpha channel that works with your system.
Older mac users who can not update QuickTime can enable the PNG quicktime codec by opening terminal and typing:qtdefaults write LegacyVideoCodecs ApplePNG enabled
( Or they can install Perian. )Install / Update Quicktime