Hybreath, that is because you are converting from a high frame rate to a lower frame rate so some frames get dropped. AMV can only manage 16fps at best whilst most other video formats are 25-30 fps. To stop this you need to pre-process your video and lower the frame rate. I use virtualDub because it is quite quick and you can also resize, crop and adjust your video before conversion. You can download VirtualDub
HERE and there is a guide to using it
HERE. To find out what frame rate your AMV files are converting at play one on your PC with the AMV Player and right click on the picture while it is running and select properties and you will see the details. If you then convert with VirtualDub and set the same frame rate your AMV will no longer skip.