Slow Motion GONE when uploaded to YouTube

I am a movie and saved it as a MP4 (and mov) and the last 1min I made in to slow motion. This is just clips taken from home videos (off a DVD). The movie, once saved is fine. I uploaded it to YouTube and the YouTube video of it, is shorter cause it doesn't show the slow motion part in slow motion but it the "real time" speed. I re-saved it as other type (mov) and something. I don't see how this happens or why! The change is speed causes the music on the video not to end at the time I wanted. I need to it to play the slow motion like it was made to do. The YouTube run time for the video is 3:22 but the file on my harddive is 3:58.
I even re-downloaded it off a file hosting site to see if that helped.
Any ideas?