issue 1 - you should be able to go to the media settings page of the website and under "Your Pogoplug creates previews of pictures, movies and music from the files on your hard drive to make sure that you can view and share them across all web browsers and mobile devices." you should see all your attached drives. Next to the drive with the video, click the settings button, and in the Media Processing Options dialog set "Allow Pogoplug to optimize videos for playback:" to full transcode.

As to why some videos play on PC but not on Android, it's likely because your PC can read those formats, but Android cannot. Motorola has a list of supported media formats here
http://www.motorola.com/Consumers/US-EN/Consumer-Product-and-Services/Mobile-...