The "Windows Mobile 6 Professional Emulator" has a low-resolution display. Your physical device might be a hi-res device, which might explain the rendering difference. There is a "Windows Mobile 6 VGA Profesional Emulator" which has a high-res display - try running your app on the VGA emulator and see if it renders correctly. Note: you probably don't want to use the Square emulators - these have pretty non-standard square screens.
If this is the issue, try setting the AutoScaleMode on the Windows Mobile Form to AutoScaleMode.Dpi rather than AutoScaleMode.Inherit. This is a property of the Form itself (you'll need to set this on every form in your app, unless you have some sort of inheritance structure setup). The Dpi setting tells Windows Mobile to autoscale the form based on screen resolution. The default setting Inherit tells the form to use the AutoScaleMode of its parent form, but if it doesn't have a parent, it defaults to no scaling.