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Without seeing your UI layout its hard to say what might causing your layout problem. The first place to start is ensure that you are designing your screens to work on different size displays. Please see this guide which illustrates how to use the auto-resize property: http://www.genuitec.com/mobile/docs/advancedUIDesign/advancedUIDesign.html
If you have problems after reading the guide and adjusting your map’s layout please post screenshots and an example design file .mobi for us to investigate.