nottoc, Most video run at 25-30 fps these amv depending on your settings run 10-16. The Converter is not terribly good at lowering the frame rate and tends to drop large chunks of frames to do this whiich is why you see the skip every second or so as the frames are dropped,. The way to overcome this is by pre-processing your video through an alternate video encoder prior to AMV conversion. Doing this you can resize, crop and reset the frame rate to match your AMV conversions, then you will find you final AMV video smoother and better quality.
You will find a few different Video Encoders in the download section that will do this for you. I personally use VirtualDub
http://www.mympxplayer.org/virtualdub-mpeg2-df370.html
Let me know what size your players screen is and I will send you a settings profile.