Moved to Gen AMV.
This actually has nothing to do with the software that you're using, but rather the music (or even possibly the anime) you used in your video. Youtube is taking your video, doing some hardcore math, figuring out what source(s) are in your video, and then asks the copyright holders if they want to block, show ads on your video, or do something else.
I'll also take this time to mention that you don't have to worry about your video being taken down if you upload here. Uploading is more involved (takes more steps) here than it is at youtube, but there are guides to help you with that. (Moonslayer's uploading guide
) (My using FTP guide