I don't think there is a difference between the .flv file used for true streaming and .flv used for progressive download. The difference is the capabilities of the server. The same is true for Windows video files. You can use .wmv to stream or progressive download.
I have a flash media server but the videos I am converting do not support this ability
I don't understand... are you able to convert your videos to .flvs? When you say you have a Flash Media Server, have you used it to stream other videos? If so what type? Is this your server or are you using a hosting service?
Seems like if your Flash Media Server doesn't stream regular .flvs, then there's a problem with the server, not the file type. Of course, you still need a Flash player on the Web page to capture the particular stream coming from the server.