the video will be saved in the correct folder, but the video won't show up.
Just so we're on the same page, do you mean that you are able to upload the .flvs to a folder using ftp and they won't show up when you try to play them in a post? Or do you mean that you still can not get them uploaded to a folder using ftp? :-)
Assuming that you are successful at uploading the movies,try this:
Create a new folder in the root of your blog. Name it video. Using an ftp client, upload an .flv movie to the video folder. For the sake of example, lets say you named the movie "mytest.flv". If that is successful... if the movie is now in the video folder, then write a post and insert the movie like this; (because you are using the FLV Embed plugin, make sure it is correctly uploaded and activated),
[flv:/video/mytest.flv 480 360]
Now publish the post and the movie and player should be visible.