Unfortunately, our importer currently assumes a 4:3 aspect ratio on all slides. The only ways around this are to either reformat the slides that aren't going in as you expect them to, and reimport, or to recreate the slide using myUdutu. Of the two options, we recommend using the second - it's fairly quick and easy to use the templates of myUdutu to reproduce the intent of any Powerpoint slide.
We have plans to revamp our powerpoint import utility later this summer. We'll be using a third-party tool that will be able to bring in non-standard formats, as well as preserve all animations, transitions, flash, and audio.