Problems with Kono Minikukumo Utsukushii Sekai

I seem to be having some strange problem with my video. Any of these that I watch seem to be missing from the top and bottom. The bottom is cut off just around the middle of the subtitiles and the top I'm not sure where. Makes watching it very hard when you have to guess which letter is which. Has anyone else had this problem or is it just me. Also I noticed that if I open it up in virtualdub it seems to be just fine, but I can't re-encode it without it screwing up. Thanks for any help